PDBsum entry: 1svc

Transcription/DNA

PDB-id

1svc

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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Protein chain

DNA/RNA

Waters ×63

* Residue conservation analysis

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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

Biological unit:

Dimer (from PDB file)

UniProt:

P19838 (NFKB1_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

968 a.a.

Struc:

311 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

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

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Key reference

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

19098713 A.J.Fusco, D.B.Huang, D.Miller, V.Y.Wang, D.Vu, and G.Ghosh (2009).
NF-kappaB p52:RelB heterodimer recognizes two classes of kappaB sites with two distinct modes.

EMBO Rep, 10, 152-159.

20066092 A.Oeckinghaus, and S.Ghosh (2009).
The NF-kappaB family of transcription factors and its regulation.

Cold Spring Harbor Perspect Biol, 1, a000034.

19301309 D.A.Benitez, M.A.Hermoso, E.Pozo-Guisado, P.M.Fernández-Salguero, and E.A.Castellón (2009).
Regulation of cell survival by resveratrol involves inhibition of NF kappaB-regulated gene expression in prostate cancer cells.

Prostate, 69, 1045-1054.

19806632 L.Piccagli, E.Fabbri, M.Borgatti, N.Bianchi, V.Bezzerri, I.Mancini, E.Nicolis, C.M.Dechecchi, I.Lampronti, G.Cabrini, and R.Gambari (2009).
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.

ChemMedChem, 4, 2024-2033.

19887633 S.Bergqvist, V.Alverdi, B.Mengel, A.Hoffmann, G.Ghosh, and E.A.Komives (2009).
Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha.

Proc Natl Acad Sci U S A, 106, 19328-19333.

20066103 T.Huxford, and G.Ghosh (2009).
A structural guide to proteins of the NF-kappaB signaling module.

Cold Spring Harbor Perspect Biol, 1, a000075.

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.

18768082 L.Piccagli, E.Fabbri, M.Borgatti, V.Bezzerri, I.Mancini, E.Nicolis, M.C.Dechecchi, I.Lampronti, G.Cabrini, and R.Gambari (2008).
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.

17574024 D.Panne, T.Maniatis, and S.C.Harrison (2007).
An atomic model of the interferon-beta enhanceosome.

Cell, 129, 1111-1123.

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.

EMBO J, 26, 3826-3835.

17072323 A.Hoffmann, G.Natoli, and G.Ghosh (2006).
Transcriptional regulation via the NF-kappaB signaling module.

Oncogene, 25, 6706-6716.

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.

Biochemistry (Mosc), 70, 1212-1222.

15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.

Annu Rev Biophys Biomol Struct, 34, 379-398.

15908994 D.A.Dean, D.D.Strong, and W.E.Zimmer (2005).
Nuclear entry of nonviral vectors.

Gene Ther, 12, 881-890.

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.

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

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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

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.

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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.

J Biol Chem, 277, 21851-21861.

12034831 R.Crinelli, M.Bianchi, L.Gentilini, and M.Magnani (2002).
Design and characterization of decoy oligonucleotides containing locked nucleic acids.

Nucleic Acids Res, 30, 2435-2443.

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.

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.

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.

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.

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.

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.

EMBO J, 19, 4712-4722.

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

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.

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.

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.

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.

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

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.

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 code: 1ram

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.

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.

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.

Annu Rev Immunol, 14, 649-683.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 code is shown on the right.