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Transcription/DNA PDB id
1svc
Jmol
Contents
Protein chain
311 a.a. *
DNA/RNA
Waters ×63
* Residue conservation analysis
PDB id:
1svc
Name: Transcription/DNA
Title: Nfkb p50 homodimer bound to DNA
Structure: DNA (5'- d( Ap Gp Ap Tp Gp Gp Gp Gp Ap Ap Tp Cp Cp Cp Cp Tp A p Gp A)-3'). Chain: d. Engineered: yes. Protein (nuclear factor kappa-b (nf-kb)). Chain: p. Engineered: yes
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.225     R-free:   0.286
Authors: C.W.Mueller,S.C.Harrison
Key ref: C.W.Müller et al. (1995). Structure of the NF-kappa B p50 homodimer bound to DNA. Nature, 373, 311-317. PubMed id: 7830764 DOI: 10.1038/373311a0
Date:
27-Nov-95     Release date:   10-Jun-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19838  (NFKB1_HUMAN) -  Nuclear factor NF-kappa-B p105 subunit
Seq:
Struc: 		 
Seq:
Struc: 		968 a.a.
311 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription   2 terms 
  Biochemical function     transcription factor activity     1 term  

 

 
DOI no: 10.1038/373311a0 Nature 373:311-317 (1995)
PubMed id: 7830764  
 
 
Structure of the NF-kappa B p50 homodimer bound to DNA.
C.W.Müller, F.A.Rey, M.Sodeoka, G.L.Verdine, S.C.Harrison.
 
  ABSTRACT  
 
The structure of a large fragment of the p50 subunit of the human transcription factor NF-kappa B, bound as a homodimer to DNA, reveals that the Rel-homology region has two beta-barrel domains that grip DNA in the major groove. Both domains contact the DNA backbone. The amino-terminal specificity domain contains a recognition loop that interacts with DNA bases; the carboxy-terminal dimerization domain bears the site of I-kappa B interaction. The folds of these domains are related to immunoglobulin-like modules. The amino-terminal domain also resembles the core domain of p53.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21135870 C.Zheng, Q.Yin, and H.Wu (2011).
Structural studies of NF-κB signaling.
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21308698 K.Senthilkumar, R.Arunkumar, P.Elumalai, G.Sharmila, D.N.Gunadharini, S.Banudevi, G.Krishnamoorthy, C.S.Benson, and J.Arunakaran (2011).
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20055496 D.U.Ferreiro, and E.A.Komives (2010).
Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha.
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Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.
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20876732 N.Treiber, T.Treiber, G.Zocher, and R.Grosschedl (2010).
Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins.
  Genes Dev, 24, 2270-2275.
PDB codes: 3mln 3mlo 3mlp
20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
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Regulation of cell survival by resveratrol involves inhibition of NF kappaB-regulated gene expression in prostate cancer cells.
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19201872 F.L.Sinquett, R.L.Dryer, V.Marcelli, A.Batheja, and L.R.Covey (2009).
Single nucleotide changes in the human Igamma1 and Igamma4 promoters underlie different transcriptional responses to CD40.
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19683540 J.C.Stroud, A.Oltman, A.Han, D.L.Bates, and L.Chen (2009).
Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.
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PDB code: 3gut
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Virtual Screening against p50 NF-kappaB Transcription Factor for the Identification of Inhibitors of the NF-kappaB-DNA Interaction and Expression of NF-kappaB Upregulated Genes.
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19887633 S.Bergqvist, V.Alverdi, B.Mengel, A.Hoffmann, G.Ghosh, and E.A.Komives (2009).
Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha.
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  20066103 T.Huxford, and G.Ghosh (2009).
A structural guide to proteins of the NF-kappaB signaling module.
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18462673 D.L.Bates, K.K.Barthel, Y.Wu, R.Kalhor, J.C.Stroud, M.J.Giffin, and L.Chen (2008).
Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element.
  Structure, 16, 684-694.
PDB code: 2o93
18206362 D.Panne (2008).
The enhanceosome.
  Curr Opin Struct Biol, 18, 236-242.  
17959673 H.Guan, J.Jiao, and R.P.Ricciardi (2008).
Tumorigenic adenovirus type 12 E1A inhibits phosphorylation of NF-kappaB by PKAc, causing loss of DNA binding and transactivation.
  J Virol, 82, 40-48.  
  19967061 J.H.Lee, C.H.Kim, G.H.Seo, J.Lee, J.H.Kim, D.G.Kim, and Y.S.Ahn (2008).
Heparin Attenuates the Expression of TNFalpha-induced Cerebral Endothelial Cell Adhesion Molecule.
  Korean J Physiol Pharmacol, 12, 231-236.  
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Docking of molecules identified in bioactive medicinal plants extracts into the p50 NF-kappaB transcription factor: correlation with inhibition of NF-kappaB/DNA interactions and inhibitory effects on IL-8 gene expression.
  BMC Struct Biol, 8, 38.  
18175145 M.Gauthier, and B.M.Degnan (2008).
The transcription factor NF-kappaB in the demosponge Amphimedon queenslandica: insights on the evolutionary origin of the Rel homology domain.
  Dev Genes Evol, 218, 23-32.  
18337505 S.Zhang, V.Metelev, D.Tabatadze, P.C.Zamecnik, and A.Bogdanov (2008).
Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein-DNA interactions.
  Proc Natl Acad Sci U S A, 105, 4156-4161.  
18729495 Z.Yang, G.Sahay, S.Sriadibhatla, and A.V.Kabanov (2008).
Amphiphilic block copolymers enhance cellular uptake and nuclear entry of polyplex-delivered DNA.
  Bioconjug Chem, 19, 1987-1994.  
17574024 D.Panne, T.Maniatis, and S.C.Harrison (2007).
An atomic model of the interferon-beta enhanceosome.
  Cell, 129, 1111-1123.
PDB codes: 2o61 2o6g
17727632 F.D.Lubin, Y.Ren, X.Xu, and A.E.Anderson (2007).
Nuclear factor-kappa B regulates seizure threshold and gene transcription following convulsant stimulation.
  J Neurochem, 103, 1381-1395.  
17660749 M.S.Busse, C.P.Arnold, P.Towb, J.Katrivesis, and S.A.Wasserman (2007).
A kappaB sequence code for pathway-specific innate immune responses.
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Transcriptional regulation via the NF-kappaB signaling module.
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16336179 A.S.Romanenkov, A.A.Ustyugov, T.S.Zatsepin, A.A.Nikulova, I.V.Kolesnikov, V.G.Metelev, T.S.Oretskaya, and E.A.Kubareva (2005).
Analysis of DNA-protein interactions in complexes of transcription factor NF-kappaB with DNA.
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15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.
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15908994 D.A.Dean, D.D.Strong, and W.E.Zimmer (2005).
Nuclear entry of nonviral vectors.
  Gene Ther, 12, 881-890.  
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NF-kappaB RelB forms an intertwined homodimer.
  Structure, 13, 1365-1373.
PDB codes: 1zk9 1zka
15969767 D.H.Dreyfus, M.Nagasawa, E.W.Gelfand, and L.Y.Ghoda (2005).
Modulation of p53 activity by IkappaBalpha: evidence suggesting a common phylogeny between NF-kappaB and p53 transcription factors.
  BMC Immunol, 6, 12.  
15843800 G.Natoli, S.Saccani, D.Bosisio, and I.Marazzi (2005).
Interactions of NF-kappaB with chromatin: the art of being at the right place at the right time.
  Nat Immunol, 6, 439-445.  
16192280 M.S.Choi, M.C.Kim, J.H.Yoo, B.C.Moon, S.C.Koo, B.O.Park, J.H.Lee, Y.D.Koo, H.J.Han, S.Y.Lee, W.S.Chung, C.O.Lim, and M.J.Cho (2005).
Isolation of a calmodulin-binding transcription factor from rice (Oryza sativa L.).
  J Biol Chem, 280, 40820-40831.  
15215520 C.H.Croy, S.Bergqvist, T.Huxford, G.Ghosh, and E.A.Komives (2004).
Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution.
  Protein Sci, 13, 1767-1777.  
15269206 D.Angelov, F.Lenouvel, F.Hans, C.W.Müller, P.Bouvet, J.Bednar, E.N.Moudrianakis, J.Cadet, and S.Dimitrov (2004).
The histone octamer is invisible when NF-kappaB binds to the nucleosome.
  J Biol Chem, 279, 42374-42382.  
15296742 D.Y.Chirgadze, M.Demydchuk, M.Becker, S.Moran, and M.Paoli (2004).
Snapshot of protein structure evolution reveals conservation of functional dimerization through intertwined folding.
  Structure, 12, 1489-1494.
PDB codes: 1u36 1u3j 1u3y 1u3z 1u41 1u42
15102445 G.Ghosh, D.B.Huang, and T.Huxford (2004).
Molecular mimicry of the NF-kappaB DNA target site by a selected RNA aptamer.
  Curr Opin Struct Biol, 14, 21-27.  
14573596 H.Pang, M.Bartlam, Q.Zeng, H.Miyatake, T.Hisano, K.Miki, L.L.Wong, G.F.Gao, and Z.Rao (2004).
Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor.
  J Biol Chem, 279, 1491-1498.
PDB code: 1j1l
14990752 J.Linnell, R.Mott, S.Field, D.P.Kwiatkowski, J.Ragoussis, and I.A.Udalova (2004).
Quantitative high-throughput analysis of transcription factor binding specificities.
  Nucleic Acids Res, 32, e44.  
15297877 R.A.Kovall, and W.A.Hendrickson (2004).
Crystal structure of the nuclear effector of Notch signaling, CSL, bound to DNA.
  EMBO J, 23, 3441-3451.
PDB code: 1ttu
14532125 A.Hoffmann, T.H.Leung, and D.Baltimore (2003).
Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities.
  EMBO J, 22, 5530-5539.  
12588973 B.Rayet, Y.Fan, and C.Gélinas (2003).
Mutations in the v-Rel transactivation domain indicate altered phosphorylation and identify a subset of NF-kappaB-regulated cell death inhibitors important for v-Rel transforming activity.
  Mol Cell Biol, 23, 1520-1533.  
12870843 D.Angelov, M.Charra, C.W.Müller, J.Cadet, and S.Dimitrov (2003).
Solution study of the NF-kappaB p50-DNA complex by UV laser protein-DNA cross-linking.
  Photochem Photobiol, 77, 592-596.  
12886018 D.B.Huang, D.Vu, L.A.Cassiday, J.M.Zimmerman, L.J.Maher, and G.Ghosh (2003).
Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer.
  Proc Natl Acad Sci U S A, 100, 9268-9273.
PDB code: 1ooa
12624092 H.R.Mott, D.Nietlispach, L.J.Hopkins, G.Mirey, J.H.Camonis, and D.Owen (2003).
Structure of the GTPase-binding domain of Sec5 and elucidation of its Ral binding site.
  J Biol Chem, 278, 17053-17059.
PDB code: 1hk6
12949491 L.Jin, P.Sliz, L.Chen, F.Macián, A.Rao, P.G.Hogan, and S.C.Harrison (2003).
An asymmetric NFAT1 dimer on a pseudo-palindromic kappa B-like DNA site.
  Nat Struct Biol, 10, 807-811.
PDB code: 1pzu
12807880 L.Lin, and M.Kobayashi (2003).
Stability of the Rel homology domain is critical for generation of NF-kappa B p50 subunit.
  J Biol Chem, 278, 31479-31485.  
12949493 M.J.Giffin, J.C.Stroud, D.L.Bates, K.D.von Koenig, J.Hardin, and L.Chen (2003).
Structure of NFAT1 bound as a dimer to the HIV-1 LTR kappa B element.
  Nat Struct Biol, 10, 800-806.
PDB code: 1p7h
12947093 S.Hou, H.Guan, and R.P.Ricciardi (2003).
Phosphorylation of serine 337 of NF-kappaB p50 is critical for DNA binding.
  J Biol Chem, 278, 45994-45998.  
12736320 X.Yang, X.Li, T.W.Prow, L.M.Reece, S.E.Bassett, B.A.Luxon, N.K.Herzog, J.Aronson, R.E.Shope, J.F.Leary, and D.G.Gorenstein (2003).
Immunofluorescence assay and flow-cytometry selection of bead-bound aptamers.
  Nucleic Acids Res, 31, e54.  
12644465 Y.Nam, A.P.Weng, J.C.Aster, and S.C.Blacklow (2003).
Structural requirements for assembly of the CSL.intracellular Notch1.Mastermind-like 1 transcriptional activation complex.
  J Biol Chem, 278, 21232-21239.  
11967310 A.S.Liss, and H.R.Bose (2002).
Mutational analysis of the v-Rel dimerization interface reveals a critical role for v-Rel homodimers in transformation.
  J Virol, 76, 4928-4939.  
11970948 B.Berkowitz, D.B.Huang, F.E.Chen-Park, P.B.Sigler, and G.Ghosh (2002).
The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site.
  J Biol Chem, 277, 24694-24700.
PDB codes: 1le5 1le9
  12005436 C.R.Escalante, L.Shen, D.Thanos, and A.K.Aggarwal (2002).
Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter.
  Structure, 10, 383-391.
PDB code: 2i9t
11970949 F.E.Chen-Park, D.B.Huang, B.Noro, D.Thanos, and G.Ghosh (2002).
The kappa B DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription.
  J Biol Chem, 277, 24701-24708.
PDB code: 1lei
12048232 I.A.Udalova, R.Mott, D.Field, and D.Kwiatkowski (2002).
Quantitative prediction of NF-kappa B DNA-protein interactions.
  Proc Natl Acad Sci U S A, 99, 8167-8172.  
11780147 J.C.Stroud, C.Lopez-Rodriguez, A.Rao, and L.Chen (2002).
Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.
  Nat Struct Biol, 9, 90-94.
PDB code: 1imh
11877450 J.H.Lee, T.H.Koo, B.Y.Hwang, and J.J.Lee (2002).
Kaurane diterpene, kamebakaurin, inhibits NF-kappa B by directly targeting the DNA-binding activity of p50 and blocks the expression of antiapoptotic NF-kappa B target genes.
  J Biol Chem, 277, 18411-18420.  
11985582 J.Jin, X.Chen, Y.Zhou, M.Bartlam, Q.Guo, Y.Liu, Y.Sun, Y.Gao, S.Ye, G.Li, Z.Rao, B.Qiang, and J.Yuan (2002).
Crystal structure of the catalytic domain of a human thioredoxin-like protein.
  Eur J Biochem, 269, 2060-2068.
PDB code: 1gh2
12411490 J.S.Lamoureux, D.Stuart, R.Tsang, C.Wu, and J.N.Glover (2002).
Structure of the sporulation-specific transcription factor Ndt80 bound to DNA.
  EMBO J, 21, 5721-5732.
PDB codes: 1mn4 1mnn
12384592 K.Wecker, M.C.Bonnet, E.F.Meurs, and M.Delepierre (2002).
The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex.
  Nucleic Acids Res, 30, 4452-4459.  
11988749 M.Rape, and S.Jentsch (2002).
Taking a bite: proteasomal protein processing.
  Nat Cell Biol, 4, E113-E116.  
11925432 N.Bouché, A.Scharlat, W.Snedden, D.Bouchez, and H.Fromm (2002).
A novel family of calmodulin-binding transcription activators in multicellular organisms.
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12034831 R.Crinelli, M.Bianchi, L.Gentilini, and M.Magnani (2002).
Design and characterization of decoy oligonucleotides containing locked nucleic acids.
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11870918 R.E.Speight, D.J.Hart, and J.M.Blackburn (2002).
Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner.
  J Mol Recognit, 15, 19-26.  
11983155 S.Ghosh, and M.Karin (2002).
Missing pieces in the NF-kappaB puzzle.
  Cell, 109, S81-S96.  
12077338 S.Jia, R.D.Flores-Saaib, and A.J.Courey (2002).
The Dorsal Rel homology domain plays an active role in transcriptional regulation.
  Mol Cell Biol, 22, 5089-5099.  
12384578 S.P.Montano, M.L.Coté, I.Fingerman, M.Pierce, A.K.Vershon, and M.M.Georgiadis (2002).
Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast.
  Proc Natl Acad Sci U S A, 99, 14041-14046.
PDB codes: 1m6u 1m7u
12213807 T.Nishi, N.Shimizu, M.Hiramoto, I.Sato, Y.Yamaguchi, M.Hasegawa, S.Aizawa, H.Tanaka, K.Kataoka, H.Watanabe, and H.Handa (2002).
Spatial redox regulation of a critical cysteine residue of NF-kappa B in vivo.
  J Biol Chem, 277, 44548-44556.  
12466564 X.Yang, S.E.Bassett, X.Li, B.A.Luxon, N.K.Herzog, R.E.Shope, J.Aronson, T.W.Prow, J.F.Leary, R.Kirby, A.D.Ellington, and D.G.Gorenstein (2002).
Construction and selection of bead-bound combinatorial oligonucleoside phosphorothioate and phosphorodithioate aptamer libraries designed for rapid PCR-based sequencing.
  Nucleic Acids Res, 30, e132.  
12465027 Y.S.Day, S.L.Bacon, Z.Hughes-Thomas, J.M.Blackburn, and J.D.Sutherland (2002).
Mutational analysis of the kinetics and thermodynamics of transcription factor NF-kappaB homodimerisation.
  Chembiochem, 3, 1192-1199.  
11741530 C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.
  Mol Cell, 8, 937-946.  
11707390 F.Michel, M.Soler-Lopez, C.Petosa, P.Cramer, U.Siebenlist, and C.W.Müller (2001).
Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family.
  EMBO J, 20, 6180-6190.
PDB codes: 1k1a 1k1b
11264458 G.Powis, and W.R.Montfort (2001).
Properties and biological activities of thioredoxins.
  Annu Rev Pharmacol Toxicol, 41, 261-295.  
11441809 G.Powis, and W.R.Montfort (2001).
Properties and biological activities of thioredoxins.
  Annu Rev Biophys Biomol Struct, 30, 421-455.  
11344309 I.A.Graef, J.M.Gastier, U.Francke, and G.R.Crabtree (2001).
Evolutionary relationships among Rel domains indicate functional diversification by recombination.
  Proc Natl Acad Sci U S A, 98, 5740-5745.  
11319766 J.Qiu, M.R.Grafe, S.M.Schmura, J.N.Glasgow, T.A.Kent, D.K.Rassin, and J.R.Perez-Polo (2001).
Differential NF-kappa B regulation of bcl-x gene expression in hippocampus and basal forebrain in response to hypoxia.
  J Neurosci Res, 64, 223-234.  
  11590020 R.E.Speight, D.J.Hart, J.D.Sutherland, and J.M.Blackburn (2001).
A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins.
  Chem Biol, 8, 951-965.  
11257229 T.H.Tahirov, T.Inoue-Bungo, H.Morii, A.Fujikawa, M.Sasaki, K.Kimura, M.Shiina, K.Sato, T.Kumasaka, M.Yamamoto, S.Ishii, and K.Ogata (2001).
Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta.
  Cell, 104, 755-767.
PDB codes: 1hjb 1hjc 1io4
  10745017 E.Conti, and J.Kuriyan (2000).
Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha.
  Structure, 8, 329-338.
PDB codes: 1ee4 1ee5
10949036 E.J.Enemark, G.Chen, D.E.Vaughn, A.Stenlund, and L.Joshua-Tor (2000).
Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus.
  Mol Cell, 6, 149-158.
PDB code: 1f08
10970869 F.Macián, C.García-Rodríguez, and A.Rao (2000).
Gene expression elicited by NFAT in the presence or absence of cooperative recruitment of Fos and Jun.
  EMBO J, 19, 4783-4795.  
10734220 G.C.Pérez-Alvarado, A.Munnerlyn, H.J.Dyson, R.Grosschedl, and P.E.Wright (2000).
Identification of the regions involved in DNA binding by the mouse PEBP2alpha protein.
  FEBS Lett, 470, 125-130.  
  11035260 G.Powis, D.Mustacich, and A.Coon (2000).
The role of the redox protein thioredoxin in cell growth and cancer.
  Free Radic Biol Med, 29, 312-322.  
10713070 J.P.Menetski (2000).
The structure of the nuclear factor-kappaB protein-DNA complex varies with DNA-binding site sequence.
  J Biol Chem, 275, 7619-7625.  
11213487 J.Qin, Y.Yang, A.Velyvis, and A.Gronenborn (2000).
Molecular views of redox regulation: three-dimensional structures of redox regulatory proteins and protein complexes.
  Antioxid Redox Signal, 2, 827-840.  
10970863 L.Lin, G.N.DeMartino, and W.C.Greene (2000).
Cotranslational dimerization of the Rel homology domain of NF-kappaB1 generates p50-p105 heterodimers and is required for effective p50 production.
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10837071 M.Karin, and Y.Ben-Neriah (2000).
Phosphorylation meets ubiquitination: the control of NF-[kappa]B activity.
  Annu Rev Immunol, 18, 621-663.  
10784442 P.Cramer, D.A.Bushnell, J.Fu, A.L.Gnatt, B.Maier-Davis, N.E.Thompson, R.R.Burgess, A.M.Edwards, P.R.David, and R.D.Kornberg (2000).
Architecture of RNA polymerase II and implications for the transcription mechanism.
  Science, 288, 640-649.
PDB code: 1en0
  10801482 Y.Q.Chen, L.L.Sengchanthalangsy, A.Hackett, and G.Ghosh (2000).
NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets.
  Structure, 8, 419-428.  
10410794 C.Wolberger (1999).
Multiprotein-DNA complexes in transcriptional regulation.
  Annu Rev Biophys Biomol Struct, 28, 29-56.  
15992127 D.Kletsas, and A.G.Papavassiliou (1999).
The therapeutic potential of targeting drugs at transcription factors.
  Expert Opin Investig Drugs, 8, 737-746.  
  10072384 E.A.Drier, L.H.Huang, and R.Steward (1999).
Nuclear import of the Drosophila Rel protein Dorsal is regulated by phosphorylation.
  Genes Dev, 13, 556-568.  
10585435 F.Chen, L.M.Demers, V.Vallyathan, Y.Lu, V.Castranova, and X.Shi (1999).
Involvement of 5'-flanking kappaB-like sites within bcl-x gene in silica-induced Bcl-x expression.
  J Biol Chem, 274, 35591-35595.  
  10022897 H.Chan, D.P.Bartos, and L.B.Owen-Schaub (1999).
Activation-dependent transcriptional regulation of the human Fas promoter requires NF-kappaB p50-p65 recruitment.
  Mol Cell Biol, 19, 2098-2108.  
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
10485885 J.M.Brickman, M.Adam, and M.Ptashne (1999).
Interactions between an HMG-1 protein and members of the Rel family.
  Proc Natl Acad Sci U S A, 96, 10679-10683.  
10336463 J.P.Yang, M.Hori, T.Sanda, and T.Okamoto (1999).
Identification of a novel inhibitor of nuclear factor-kappaB, RelA-associated inhibitor.
  J Biol Chem, 274, 15662-15670.  
10488136 K.Hirota, M.Murata, Y.Sachi, H.Nakamura, J.Takeuchi, K.Mori, and J.Yodoi (1999).
Distinct roles of thioredoxin in the cytoplasm and in the nucleus. A two-step mechanism of redox regulation of transcription factor NF-kappaB.
  J Biol Chem, 274, 27891-27897.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10212261 L.A.Dickinson, J.W.Trauger, E.E.Baird, P.B.Dervan, B.J.Graves, and J.M.Gottesfeld (1999).
Inhibition of Ets-1 DNA binding and ternary complex formation between Ets-1, NF-kappaB, and DNA by a designed DNA-binding ligand.
  J Biol Chem, 274, 12765-12773.  
10047576 L.Chen (1999).
Combinatorial gene regulation by eukaryotic transcription factors.
  Curr Opin Struct Biol, 9, 48-55.  
10074372 L.L.Lebruska, and L.J.Maher (1999).
Selection and characterization of an RNA decoy for transcription factor NF-kappa B.
  Biochemistry, 38, 3168-3174.  
10581254 M.Chiadmi, A.Navaza, M.Miginiac-Maslow, J.P.Jacquot, and J.Cherfils (1999).
Redox signalling in the chloroplast: structure of oxidized pea fructose-1,6-bisphosphate phosphatase.
  EMBO J, 18, 6809-6815.
PDB codes: 1d9q 1dbz 1dcu
10223295 M.H.Seto, H.L.Liu, D.A.Zajchowski, and M.Whitlow (1999).
Protein fold analysis of the B30.2-like domain.
  Proteins, 35, 235-249.  
9988771 M.Reuter, J.Schneider-Mergener, D.Kupper, A.Meisel, P.Mackeldanz, D.H.Krüger, and C.Schroeder (1999).
Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires.
  J Biol Chem, 274, 5213-5221.  
  10493576 M.Young, K.Kirshenbaum, K.A.Dill, and S.Highsmith (1999).
Predicting conformational switches in proteins.
  Protein Sci, 8, 1752-1764.  
  10511458 N.B.Blatt, and G.D.Glick (1999).
Anti-DNA autoantibodies and systemic lupus erythematosus.
  Pharmacol Ther, 83, 125-139.  
  10425685 P.Cramer, A.Varrot, C.Barillas-Mury, F.C.Kafatos, and C.W.Müller (1999).
Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA.
  Structure, 7, 841-852.
PDB code: 1bvo
  10368277 P.Cramer, and C.W.Müller (1999).
A firm hand on NFkappaB: structures of the IkappaBalpha-NFkappaB complex.
  Structure, 7, R1-R6.  
10431175 S.G.Sedgwick, and S.J.Smerdon (1999).
The ankyrin repeat: a diversity of interactions on a common structural framework.
  Trends Biochem Sci, 24, 311-316.  
10426425 S.Natori, H.Shiraishi, S.Hori, and A.Kobayashi (1999).
The roles of Sarcophaga defense molecules in immunity and metamorphosis.
  Dev Comp Immunol, 23, 317-328.  
11232330 T.Huxford, S.Malek, and G.Ghosh (1999).
Structure and mechanism in NF-kappa B/I kappa B signaling.
  Cold Spring Harb Symp Quant Biol, 64, 533-540.  
10400641 X.M.Zhang, and G.L.Verdine (1999).
A small region in HMG I(Y) is critical for cooperation with NF-kappaB on DNA.
  J Biol Chem, 274, 20235-20243.  
10612599 X.Yang, S.Fennewald, B.A.Luxon, J.Aronson, N.K.Herzog, and D.G.Gorenstein (1999).
Aptamers containing thymidine 3'-O-phosphorodithioates: synthesis and binding to nuclear factor-kappaB.
  Bioorg Med Chem Lett, 9, 3357-3362.  
9755455 A.G.Papavassiliou (1998).
Transcription-factor-modulating agents: precision and selectivity in drug design.
  Mol Med Today, 4, 358-366.  
9873704 A.Kittaka, T.Kuze, T.Asakura, K.Ito, T.Miyasaka, and J.Inoue (1998).
Oligonucleotides bearing 5-formyl-2'-O-methyluridine: preference in binding affinity to the NF-kappa B (p50)2 homo- and p50/p65 heterodimers.
  Bioorg Med Chem Lett, 8, 3207-3210.  
  9667910 A.M.Baranger (1998).
Accessory factor-bZIP-DNA interactions.
  Curr Opin Chem Biol, 2, 18-23.  
  9794820 C.Wolberger (1998).
Combinatorial transcription factors.
  Curr Opin Genet Dev, 8, 552-559.  
9799727 D.Rhodes, and J.W.Schwabe (1998).
Signal transduction: fast lane to transcriptional activation.
  Curr Biol, 8, R765-R767.  
9794241 E.S.Masuda, R.Imamura, Y.Amasaki, K.Arai, and N.Arai (1998).
Signalling into the T-cell nucleus: NFAT regulation.
  Cell Signal, 10, 599-611.  
  9488441 F.Hirano, H.Tanaka, Y.Hirano, M.Hiramoto, H.Handa, I.Makino, and C.Scheidereit (1998).
Functional interference of Sp1 and NF-kappaB through the same DNA binding site.
  Mol Cell Biol, 18, 1266-1274.  
  9488436 I.Luque, and C.Gélinas (1998).
Distinct domains of IkappaBalpha regulate c-Rel in the cytoplasm and in the nucleus.
  Mol Cell Biol, 18, 1213-1224.  
  9680181 M.E.Ginn-Pease, and R.L.Whisler (1998).
Redox signals and NF-kappaB activation in T cells.
  Free Radic Biol Med, 25, 346-361.  
9668115 M.K.Shirra, and U.Hansen (1998).
LSF and NTF-1 share a conserved DNA recognition motif yet require different oligomerization states to form a stable protein-DNA complex.
  J Biol Chem, 273, 19260-19268.  
  9566883 M.Latimer, M.K.Ernst, L.L.Dunn, M.Drutskaya, and N.R.Rice (1998).
The N-terminal domain of IkappaB alpha masks the nuclear localization signal(s) of p50 and c-Rel homodimers.
  Mol Cell Biol, 18, 2640-2649.  
9736624 M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, and S.E.Phillips (1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
  EMBO J, 17, 5466-5476.
PDB code: 1dmu
9506523 P.Zhou, L.J.Sun, V.Dötsch, G.Wagner, and G.L.Verdine (1998).
Solution structure of the core NFATC1/DNA complex.
  Cell, 92, 687-696.
PDB code: 1a66
9671298 S.Becker, B.Groner, and C.W.Müller (1998).
Three-dimensional structure of the Stat3beta homodimer bound to DNA.
  Nature, 394, 145-151.
PDB code: 1bg1
9597130 S.Ghosh, M.J.May, and E.B.Kopp (1998).
NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses.
  Annu Rev Immunol, 16, 225-260.  
9738011 S.Malek, T.Huxford, and G.Ghosh (1998).
Ikappa Balpha functions through direct contacts with the nuclear localization signals and the DNA binding sequences of NF-kappaB.
  J Biol Chem, 273, 25427-25435.  
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
9697411 T.J.Gibson, C.Ramu, C.Gemünd, and R.Aasland (1998).
The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor.
  Trends Biochem Sci, 23, 242-244.  
9630226 X.Chen, U.Vinkemeier, Y.Zhao, D.Jeruzalmi, J.E.Darnell, and J.Kuriyan (1998).
Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA.
  Cell, 93, 827-839.
PDB code: 1bf5
9437432 Y.Q.Chen, S.Ghosh, and G.Ghosh (1998).
A novel DNA recognition mode by the NF-kappa B p65 homodimer.
  Nat Struct Biol, 5, 67-73.
PDB codes: 1ram 2ram
9143705 A.Rao, C.Luo, and P.G.Hogan (1997).
Transcription factors of the NFAT family: regulation and function.
  Annu Rev Immunol, 15, 707-747.  
  9570146 C.Xia, J.K.Cheshire, H.Patel, and P.Woo (1997).
Cross-talk between transcription factors NF-kappa B and C/EBP in the transcriptional regulation of genes.
  Int J Biochem Cell Biol, 29, 1525-1539.  
  9384558 D.B.Huang, T.Huxford, Y.Q.Chen, and G.Ghosh (1997).
The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits.
  Structure, 5, 1427-1436.
PDB codes: 1bfs 1bft
9407099 D.L.Bundy, and T.W.McKeithan (1997).
Diverse effects of BCL3 phosphorylation on its modulation of NF-kappaB p52 homodimer binding to DNA.
  J Biol Chem, 272, 33132-33139.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
  9303180 I.A.Kozlov, E.A.Kubareva, M.G.Ivanovskaya, and Z.A.Shabarova (1997).
Design of new reagents on the base of DNA duplexes for irreversible inhibition of transcription factor NF-kappa B.
  Antisense Nucleic Acid Drug Dev, 7, 279-289.  
9405646 J.Yang, and R.Steward (1997).
A multimeric complex and the nuclear targeting of the Drosophila Rel protein Dorsal.
  Proc Natl Acad Sci U S A, 94, 14524-14529.  
  9271416 K.Tran, M.Merika, and D.Thanos (1997).
Distinct functional properties of IkappaB alpha and IkappaB beta.
  Mol Cell Biol, 17, 5386-5399.  
9354759 L.Jen-Jacobson (1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
  Biopolymers, 44, 153-180.  
9384586 P.Cramer, C.J.Larson, G.L.Verdine, and C.W.Müller (1997).
Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.
  EMBO J, 16, 7078-7090.
PDB code: 1a3q
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9139720 R.T.Utley, J.Côté, T.Owen-Hughes, and J.L.Workman (1997).
SWI/SNF stimulates the formation of disparate activator-nucleosome complexes but is partially redundant with cooperative binding.
  J Biol Chem, 272, 12642-12649.  
  9199307 S.Plaisance, W.Vanden Berghe, E.Boone, W.Fiers, and G.Haegeman (1997).
Recombination signal sequence binding protein Jkappa is constitutively bound to the NF-kappaB site of the interleukin-6 promoter and acts as a negative regulatory factor.
  Mol Cell Biol, 17, 3733-3743.  
8626528 A.Civil, A.Bakker, I.Rensink, S.Doerre, L.A.Aarden, and C.L.Verweij (1996).
Nuclear appearance of a factor that binds the CD28 response element within the interleukin-2 enhancer correlates with interleukin-2 production.
  J Biol Chem, 271, 8321-8327.  
8986786 A.G.Ostermeyer, E.Runko, B.Winkfield, B.Ahn, and U.M.Moll (1996).
Cytoplasmically sequestered wild-type p53 protein in neuroblastoma is relocated to the nucleus by a C-terminal peptide.
  Proc Natl Acad Sci U S A, 93, 15190-15194.  
8717528 A.S.Baldwin (1996).
The NF-kappa B and I kappa B proteins: new discoveries and insights.
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8824275 B.E.Crute, A.F.Lewis, Z.Wu, J.H.Bushweller, and N.A.Speck (1996).
Biochemical and biophysical properties of the core-binding factor alpha2 (AML1) DNA-binding domain.
  J Biol Chem, 271, 26251-26260.  
8942992 B.R.Peterson, L.J.Sun, and G.L.Verdine (1996).
A critical arginine residue mediates cooperativity in the contact interface between transcription factors NFAT and AP-1.
  Proc Natl Acad Sci U S A, 93, 13671-13676.  
  8887560 C.Barillas-Mury, A.Charlesworth, I.Gross, A.Richman, J.A.Hoffmann, and F.C.Kafatos (1996).
Immune factor Gambif1, a new rel family member from the human malaria vector, Anopheles gambiae.
  EMBO J, 15, 4691-4701.  
8691127 C.Luo, E.Burgeon, and A.Rao (1996).
Mechanisms of transactivation by nuclear factor of activated T cells-1.
  J Exp Med, 184, 141-147.  
  8668213 C.Luo, E.Burgeon, J.A.Carew, P.G.McCaffrey, T.M.Badalian, W.S.Lane, P.G.Hogan, and A.Rao (1996).
Recombinant NFAT1 (NFATp) is regulated by calcineurin in T cells and mediates transcription of several cytokine genes.
  Mol Cell Biol, 16, 3955-3966.  
8605622 C.W.Müller, F.A.Rey, and S.C.Harrison (1996).
Comparison of two different DNA-binding modes of the NF-kappa B p50 homodimer.
  Nat Struct Biol, 3, 224-227.  
  8622661 D.W.White, G.A.Pitoc, and T.D.Gilmore (1996).
Interaction of the v-Rel oncoprotein with NF-kappaB and IkappaB proteins: heterodimers of a transformation-defective v-Rel mutant and NF-2 are functional in vitro and in vivo.
  Mol Cell Biol, 16, 1169-1178.  
  8627798 E.M.Rottjakob, S.Sachdev, C.A.Leanna, T.A.McKinsey, and M.Hannink (1996).
PEST-dependent cytoplasmic retention of v-Rel by I(kappa)B-alpha: evidence that I(kappa)B-alpha regulates cellular localization of c-Rel and v-Rel by distinct mechanisms.
  J Virol, 70, 3176-3188.  
  8670842 G.Franzoso, L.Carlson, K.Brown, M.B.Daucher, P.Bressler, and U.Siebenlist (1996).
Activation of the serum response factor by p65/NF-kappaB.
  EMBO J, 15, 3403-3412.  
  8807872 H.C.Nelson, and T.H.Bestor (1996).
Base eversion and shuffling by DNA methyltransferases.
  Chem Biol, 3, 419-423.  
  8816457 H.Suyang, R.Phillips, I.Douglas, and S.Ghosh (1996).
Role of unphosphorylated, newly synthesized I kappa B beta in persistent activation of NF-kappa B.
  Mol Cell Biol, 16, 5444-5449.  
  8887665 J.C.Betts, and G.J.Nabel (1996).
Differential regulation of NF-kappaB2(p100) processing and control by amino-terminal sequences.
  Mol Cell Biol, 16, 6363-6371.  
  8736558 J.Qin, G.M.Clore, W.P.Kennedy, J.Kuszewski, and A.M.Gronenborn (1996).
The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal.
  Structure, 4, 613-620.
PDB codes: 1cqg 1cqh
8710491 J.R.Matthews, C.H.Botting, M.Panico, H.R.Morris, and R.T.Hay (1996).
Inhibition of NF-kappaB DNA binding by nitric oxide.
  Nucleic Acids Res, 24, 2236-2242.  
8550590 L.Baldi, K.Brown, G.Franzoso, and U.Siebenlist (1996).
Critical role for lysines 21 and 22 in signal-induced, ubiquitin-mediated proteolysis of I kappa B-alpha.
  J Biol Chem, 271, 376-379.  
  8628291 L.Lin, and S.Ghosh (1996).
A glycine-rich region in NF-kappaB p105 functions as a processing signal for the generation of the p50 subunit.
  Mol Cell Biol, 16, 2248-2254.  
8662809 M.A.Perrella, C.Patterson, L.Tan, S.F.Yet, C.M.Hsieh, M.Yoshizumi, and M.E.Lee (1996).
Suppression of interleukin-1beta-induced nitric-oxide synthase promoter/enhancer activity by transforming growth factor-beta1 in vascular smooth muscle cells. Evidence for mechanisms other than NF-kappaB.
  J Biol Chem, 271, 13776-13780.  
8696978 M.Chytil, and G.L.Verdine (1996).
The Rel family of eukaryotic transcription factors.
  Curr Opin Struct Biol, 6, 91.  
8631829 M.Roff, J.Thompson, M.S.Rodriguez, J.M.Jacque, F.Baleux, F.Arenzana-Seisdedos, and R.T.Hay (1996).
Role of IkappaBalpha ubiquitination in signal-induced activation of NFkappaB in vivo.
  J Biol Chem, 271, 7844-7850.  
8899295 P.Beauparlant, and J.Hiscott (1996).
Biological and biochemical inhibitors of the NF-kappa B/Rel proteins and cytokine synthesis.
  Cytokine Growth Factor Rev, 7, 175-190.  
  8887676 S.Bell, J.R.Matthews, E.Jaffray, and R.T.Hay (1996).
I(kappa)B(gamma) inhibits DNA binding of NF-kappaB p50 homodimers by interacting with residues that contact DNA.
  Mol Cell Biol, 16, 6477-6485.  
  8622655 S.Govind, E.Drier, L.H.Huang, and R.Steward (1996).
Regulated nuclear import of the Drosophila rel protein dorsal: structure-function analysis.
  Mol Cell Biol, 16, 1103-1114.  
  8622650 S.Sun, J.Elwood, and W.C.Greene (1996).
Both amino- and carboxyl-terminal sequences within I kappa B alpha regulate its inducible degradation.
  Mol Cell Biol, 16, 1058-1065.  
7773784 A.K.Aggarwal (1995).
A gripping end to NF-kappa B.
  Nat Struct Biol, 2, 184-186.  
  7565415 A.Roulston, R.Lin, P.Beauparlant, M.A.Wainberg, and J.Hiscott (1995).
Regulation of human immunodeficiency virus type 1 and cytokine gene expression in myeloid cells by NF-kappa B/Rel transcription factors.
  Microbiol Rev, 59, 481-505.  
  7735829 J.Kuriyan, and D.Thanos (1995).
Structure of the NF-kappa B transcription factor: a holistic interaction with DNA.
  Structure, 3, 135-141.  
  7788295 J.Qin, G.M.Clore, W.M.Kennedy, J.R.Huth, and A.M.Gronenborn (1995).
Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B.
  Structure, 3, 289-297.
PDB codes: 1mdi 1mdj 1mdk
7567448 J.R.Matthews, J.Nicholson, E.Jaffray, S.M.Kelly, N.C.Price, and R.T.Hay (1995).
Conformational changes induced by DNA binding of NF-kappa B.
  Nucleic Acids Res, 23, 3393-3402.  
  7584622 J.R.Matthews, and R.T.Hay (1995).
Regulation of the DNA binding activity of NF-kappa B.
  Int J Biochem Cell Biol, 27, 865-879.  
8548798 J.V.Falvo, D.Thanos, and T.Maniatis (1995).
Reversal of intrinsic DNA bends in the IFN beta gene enhancer by transcription factors and the architectural protein HMG I(Y).
  Cell, 83, 1101-1111.  
7624321 L.Shapiro, P.D.Kwong, A.M.Fannon, D.R.Colman, and W.A.Hendrickson (1995).
Considerations on the folding topology and evolutionary origin of cadherin domains.
  Proc Natl Acad Sci U S A, 92, 6793-6797.  
8597085 M.L.Schmitz (1995).
Function and activation of the transcription factor NF-kappa B in the response to toxins and pathogens.
  Toxicol Lett, 82, 407-411.  
7479760 N.Lehming, S.McGuire, J.M.Brickman, and M.Ptashne (1995).
Interactions of a Rel protein with its inhibitor.
  Proc Natl Acad Sci U S A, 92, 10242-10246.  
9415148 O.Heidenreich, S.H.Kang, X.Xu, and M.Nerenberg (1995).
Application of antisense technology to therapeutics.
  Mol Med Today, 1, 128-133.  
  7760806 R.P.Ryseck, J.Novotny, and R.Bravo (1995).
Characterization of elements determining the dimerization properties of RelB and p50.
  Mol Cell Biol, 15, 3100-3109.  
  9383407 S.K.Burley (1995).
Rel revealed: cocrystal structures of the NF-kappa B p50 homodimer.
  Chem Biol, 2, 77-81.  
7749981 T.Hoey, Y.L.Sun, K.Williamson, and X.Xu (1995).
Isolation of two new members of the NF-AT gene family and functional characterization of the NF-AT proteins.
  Immunity, 2, 461-472.  
7552992 T.S.Finco, and A.S.Baldwin (1995).
Mechanistic aspects of NF-kappa B regulation: the emerging role of phosphorylation and proteolysis.
  Immunity, 3, 263-272.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.