PDBsum entry 1vkx

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
273 a.a. *
312 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Crystal structure of the nfkb p50/p65 heterodimer complexed to the immunoglobulin kb DNA
Structure: DNA (5'-d( Tp Gp Gp Gp Gp Ap Cp Tp Tp Tp Cp C)- 3'). Chain: c. Synonym: immunoglobulin kappa b DNA. Engineered: yes. Other_details: active nf-kappa-b is a heterodimer of an about 50 kd DNA-binding subunit and the weak DNA-binding subunit p65. DNA (5'-d( Ap Gp Gp Ap Ap Ap Gp Tp Cp Cp Cp C)-
Source: Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Hetero-Dimer (from PDB file)
2.90Å     R-factor:   0.208     R-free:   0.320
Authors: F.Chen,D.B.Huang,G.Ghosh
Key ref:
F.E.Chen et al. (1998). Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature, 391, 410-413. PubMed id: 9450761 DOI: 10.1038/34956
17-Sep-97     Release date:   09-Dec-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q04207  (TF65_MOUSE) -  Transcription factor p65
549 a.a.
273 a.a.*
Protein chain
Pfam   ArchSchema ?
P25799  (NFKB1_MOUSE) -  Nuclear factor NF-kappa-B p105 subunit
971 a.a.
312 a.a.
Key:    PfamA domain  PfamB 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, DNA-dependent   1 term 
  Biochemical function     sequence-specific DNA binding transcription factor activity     1 term  


DOI no: 10.1038/34956 Nature 391:410-413 (1998)
PubMed id: 9450761  
Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA.
F.E.Chen, D.B.Huang, Y.Q.Chen, G.Ghosh.
The NF-kappaB p50/p65 heterodimer is the classical member of the Rel family of transcription factors which regulate diverse cellular functions such as immune response, cell growth, and development. Other mammalian Rel family members, including the proteins p52, proto-oncoprotein c-Rel, and RelB, all have amino-terminal Rel-homology regions (RHRs). The RHR is responsible for the dimerization, DNA binding and cytosolic localization of these proteins by virtue of complex formation with inhibitor kappaB proteins. Signal-induced removal of kappaB inhibitors allows translocation of dimers to the cell nucleus and transcriptional regulation of kappaB DNA-containing genes. NF-kappaB specifically recognizes kappaB DNA elements with a consensus sequence of 5'-GGGRNYYYCC-3' (R is an unspecified purine; Y is an unspecified pyrimidine; and N is any nucleotide). Here we report the crystal structure at 2.9 A resolution of the p50/p65 heterodimer bound to the kappaB DNA of the intronic enhancer of the immunoglobulin light-chain gene. Our structure reveals a 5-base-pair 5' subsite for p50, and a 4-base-pair 3' subsite for p65. This structure indicates why the p50/p65 heterodimer interface is stronger than that of either homodimer. A comparison of this structure with those of other Rel dimers reveals that both subunits adopt variable conformations in a DNA-sequence-dependent manner. Our results explain the different behaviour of the p50/p65 heterodimer with heterologous promoters.
  Selected figure(s)  
Figure 2.
Figure 2 The structure of the heterodimer bound on the Ig B DNA. a, Ribbon drawing of the entire complex viewed down the DNA helical axis. The p50 subunit is in green and the p65 subunit is in red. The top strand of DNA is in pink, and the bottom strand is in yellow. Drawing produced with SETOR30. b, The hydrophobic core of the dimer interface between p50 (green) and p65 (red) consists of an array of nonpolar hydrocarbons, aromatic rings and uncharged polar residues pointing from the -sheets in towards the interface. Only the -strands and seven residues contributing to the interface are displayed. Oxygens (red) and nitrogens (dark blue) are included.
Figure 3.
Figure 3 DNA contacts made by the heterodimer. a, The DNA contacts made by the p50/p65 NF- B heterodimer. Blue and green distinguish the p65 and the p50 subunits, respectively. Arrows denote hydrogen bonds; brown ovals indicate van der Waals contacts. The p50 subunit binds to the 5' five-base-pair subsite; the p65 subunit binds to the 3' four-base-pair subsite. b (top), Stereo pair of the base-specific interactions mediated by Arg 54, Arg 56, Glu 60 and His 64 of the p50 subunit. Hydrogen bonds are drawn as dashed lines between grey oxygens and dark blue nitrogens. p50 residues are green, top strand bases are yellow, while the bottom strand base is in blue. Bottom, Stereo pair of the base-specific interactions mediated by Arg 34, Arg 35, Glu 39 and Arg 187 of the p65 subunit. p65 residues are shown in green.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 391, 410-413) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 2o61 2o6g
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PDB code: 1ooa
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PDB code: 1hk6
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PDB code: 1p7h
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Phosphorylation of serine 337 of NF-kappaB p50 is critical for DNA binding.
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Regulation of c-myc gene by nitric oxide via inactivating NF-kappa B complex in P19 mouse embryonal carcinoma cells.
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Structural requirements for assembly of the CSL.intracellular Notch1.Mastermind-like 1 transcriptional activation complex.
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The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site.
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PDB codes: 1le5 1le9
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The kappa B DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription.
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PDB code: 1lei
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Quantitative prediction of NF-kappa B DNA-protein interactions.
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Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.
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PDB code: 1imh
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Structure of the sporulation-specific transcription factor Ndt80 bound to DNA.
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PDB codes: 1mn4 1mnn
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The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex.
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12456660 L.F.Chen, Y.Mu, and W.C.Greene (2002).
Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF-kappaB.
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12056891 N.R.Wurtz, J.L.Pomerantz, D.Baltimore, and P.B.Dervan (2002).
Inhibition of DNA binding by NF-kappa B with pyrrole-imidazole polyamides.
  Biochemistry, 41, 7604-7609.  
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.
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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.
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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.
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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
10781090 D.S.Straus, G.Pascual, M.Li, J.S.Welch, M.Ricote, C.H.Hsiang, L.L.Sengchanthalangsy, G.Ghosh, and C.K.Glass (2000).
15-deoxy-delta 12,14-prostaglandin J2 inhibits multiple steps in the NF-kappa B signaling pathway.
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11094063 I.A.Udalova, A.Richardson, A.Denys, C.Smith, H.Ackerman, B.Foxwell, and D.Kwiatkowski (2000).
Functional consequences of a polymorphism affecting NF-kappaB p50-p50 binding to the TNF promoter region.
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10713070 J.P.Menetski (2000).
The structure of the nuclear factor-kappaB protein-DNA complex varies with DNA-binding site sequence.
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10848607 J.V.Falvo, B.S.Parekh, C.H.Lin, E.Fraenkel, and T.Maniatis (2000).
Assembly of a functional beta interferon enhanceosome is dependent on ATF-2-c-jun heterodimer orientation.
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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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10995388 R.M.Nissen, and K.R.Yamamoto (2000).
The glucocorticoid receptor inhibits NFkappaB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain.
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10194299 C.Tisné, B.Hartmann, and M.Delepierre (1999).
NF-kappa B binding mechanism: a nuclear magnetic resonance and modeling study of a GGG --> CTC mutation.
  Biochemistry, 38, 3883-3894.
PDB codes: 3kbd 4kbd
  10022903 D.B.Kushner, and R.P.Ricciardi (1999).
Reduced phosphorylation of p50 is responsible for diminished NF-kappaB binding to the major histocompatibility complex class I enhancer in adenovirus type 12-transformed cells.
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10541551 D.Chasman, K.Cepek, P.A.Sharp, and C.O.Pabo (1999).
Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface.
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PDB code: 1cqt
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.  
10488062 M.Karin (1999).
The beginning of the end: IkappaB kinase (IKK) and NF-kappaB activation.
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The roles of Sarcophaga defense molecules in immunity and metamorphosis.
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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.
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10487755 Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, and T.Hakoshima (1999).
Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
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PDB code: 2irf
9721103 E.Zandi, Y.Chen, and M.Karin (1998).
Direct phosphorylation of IkappaB by IKKalpha and IKKbeta: discrimination between free and NF-kappaB-bound substrate.
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9727052 M.F.Smith, V.S.Carl, T.Lodie, and M.J.Fenton (1998).
Secretory interleukin-1 receptor antagonist gene expression requires both a PU.1 and a novel composite NF-kappaB/PU.1/ GA-binding protein binding site.
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The N-terminal domain of IkappaB alpha masks the nuclear localization signal(s) of p50 and c-Rel homodimers.
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9671298 S.Becker, B.Groner, and C.W.Müller (1998).
Three-dimensional structure of the Stat3beta homodimer bound to DNA.
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PDB code: 1bg1
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.  
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.