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1vkx

CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA

Method: X-RAY DIFFRACTION Dmax: 103.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (NF-KAPPA B P65 SUBUNIT)

OrganismNot specified

UniProt Q04207

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 19–291 Not recorded ;DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3') ; × 1 PROTEIN (NF-KAPPA B P50 SUBUNIT) × 1 （P25799） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.50, VAPOR DIFFUSION, HANGING DROP Resolution 2.90 Å R-free 0.320

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1VKX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BFT STRUCTURE OF NF-KB P65 HOMODIMER BOUND TO A KB SITE Deposited 1997-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 191–291（101 aa） Fragment：DIMERIZATION DOMAIN
Chain B 191–291（101 aa） Fragment：DIMERIZATION DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.294
1IKN IKAPPABALPHA/NF-KAPPAB COMPLEX Deposited 1998-11-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 19–304（286 aa） Fragment：N-TERMINAL AND DIMERIZATION DOMAINS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 2.30 Å R-free 0.277
1K3Z X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex Deposited 2001-10-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 191–326（136 aa） Fragment：p65 dimerization domain
Chain B 191–326（136 aa） Fragment：p65 dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.256
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 20–291（272 aa） Fragment：p65 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.75 Å R-free 0.293
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain E 20–291（272 aa） Fragment：p65 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.75 Å R-free 0.293
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 20–291（272 aa） Fragment：p65 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Resolution 3.00 Å R-free 0.305
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain E 20–291（272 aa） Fragment：p65 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Resolution 3.00 Å R-free 0.305
1LEI The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 20–291（272 aa） Fragment：p65 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 6.5；291 K；PEG 3350, CaCl2, sodium spermine, pH 6.5, SMALL TUBES, temperature 291K
Resolution 2.70 Å R-free 0.284
1MY5 NF-kappaB p65 subunit dimerization domain homodimer Deposited 2002-10-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 191–304（114 aa） Fragment：residues 191-304 (dimerization domain)
Chain B 191–304（114 aa） Fragment：residues 191-304 (dimerization domain)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M sodium HEPES, 0.2M sodium tartrate, 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.221
1MY7 NF-kappaB p65 subunit dimerization domain homodimer N202R mutation Deposited 2002-10-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 191–304（114 aa） Fragment：residues 191 - 304 (dimerization domain)
Chain B 191–304（114 aa） Fragment：residues 191 - 304 (dimerization domain)
Mutation：N202R Mutation：N202R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.l M sodium HEPES, 0.2 M sodium tartrate, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.49 Å R-free 0.247
1OY3 CRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX Deposited 2003-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 191–326（136 aa） Fragment：p65 dimerization domain
Chain C 191–326（136 aa） Fragment：p65 dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.247
1RAM A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER Deposited 1997-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–291（273 aa） Fragment：P65 SUBUNIT, RESIDUES 19 - 291
Chain B 19–291（273 aa） Fragment：P65 SUBUNIT, RESIDUES 19 - 291
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；crystallized from PEG 3350, CACL2, BETA-OCTYL GLUCOPYRANOSIDE, HEPES and GLYCEROL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Resolution 2.70 Å R-free 0.324
2I9T Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter Deposited 2006-09-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 19–291（273 aa） Fragment：residues 19-291
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；293 K；8% PEG 5K monomethylether, 200mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60
Resolution 2.80 Å R-free 0.288
2RAM A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER Deposited 1997-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–291（273 aa） Fragment：P65 RESIDUES 19 - 291
Chain B 19–291（273 aa） Fragment：P65 RESIDUES 19 - 291
Not recorded DTV (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.40 Å R-free 0.308
5U01 Cooperative DNA binding by two RelA dimers Deposited 2016-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 19–291（273 aa） Fragment：UNP residues 19-291
Chain B 19–291（273 aa） Fragment：UNP residues 19-291
Chain C 19–291（273 aa） Fragment：UNP residues 19-291
Chain D 19–291（273 aa） Fragment：UNP residues 19-291
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；Nacit 5.5 100mM, CaCl2 10mM, DTT 10mM, PEG 3350 15%.
Resolution 2.50 Å R-free 0.274
6GGR Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65 Deposited 2018-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–188（169 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallyzation conditions: 0.1 M Tris pH 8.3, 0.5 M LiCl and 32.5% (w/v) PEG 6000
Resolution 2.10 Å R-free 0.252
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–98（80 aa）
Chain A 191–291（101 aa）
Chain B 19–98（80 aa）
Chain B 191–291（101 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG
Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain G 19–98（80 aa）
Chain G 191–291（101 aa）
Chain H 19–98（80 aa）
Chain H 191–291（101 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG
Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain K 19–98（80 aa）
Chain K 191–291（101 aa）
Chain L 19–98（80 aa）
Chain L 191–291（101 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG
Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain O 19–98（80 aa）
Chain O 191–291（101 aa）
Chain P 19–98（80 aa）
Chain P 191–291（101 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG
Resolution 3.09 Å R-free 0.329
9BDU NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–304（286 aa） Fragment：residues 19-304
Chain B 19–304（286 aa） Fragment：residues 19-304
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, beta-octylglucoside, spermine
Resolution 2.03 Å R-free 0.273
9BDV NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–304（286 aa） Fragment：residues 19-304
Chain B 19–304（286 aa） Fragment：residues 19-304
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside
Resolution 1.90 Å R-free 0.230
9BDW NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–304（286 aa） Fragment：residues 19-304
Chain B 19–304（286 aa） Fragment：residues 19-304
Not recorded SO4 SULFATE ION × 5 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside
Resolution 1.87 Å R-free 0.227
9BDX NF-kappaB RelA homo-dimer bound to CG-centric kappaB DNA Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–304（286 aa） Fragment：residues 19-304
Chain B 19–304（286 aa） Fragment：residues 19-304
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside
Resolution 3.60 Å R-free 0.374
9E6W NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene Deposited 2024-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 19–304（286 aa） Fragment：residues 19-304
Chain B 19–304（286 aa） Fragment：residues 19-304
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Tris HCl 25mM pH 7.5, NaCl 50 mM, DTT 1 mM, MES 50 mM pH 5.5, CaCl2 2 mM, Spermidine 1 mM, b-D-octylglucopyranoside 0.05%, Ammonium chloride 50 mM, PEG3350 14%
Resolution 2.04 Å R-free 0.283

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TF65_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–273； UniProt 19–291

PROTEIN (NF-KAPPA B P50 SUBUNIT)

OrganismNot specified

UniProt P25799

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain B； UniProt 39–350 Not recorded ;DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3') ; × 1 ;DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3') ; × 1 PROTEIN (NF-KAPPA B P65 SUBUNIT) × 1 （Q04207） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.50, VAPOR DIFFUSION, HANGING DROP Resolution 2.90 Å R-free 0.320

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1VKX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BFS STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE Deposited 1997-09-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：DIMERIZATION DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.287
1IKN IKAPPABALPHA/NF-KAPPAB COMPLEX Deposited 1998-11-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 245–363（119 aa） Fragment：N-TERMINAL AND DIMERIZATION DOMAINS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 2.30 Å R-free 0.277
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 39–350（312 aa） Fragment：p50 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.75 Å R-free 0.293
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain F 39–350（312 aa） Fragment：p50 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.75 Å R-free 0.293
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 39–350（312 aa） Fragment：p50 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Resolution 3.00 Å R-free 0.305
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain F 39–350（312 aa） Fragment：p50 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Resolution 3.00 Å R-free 0.305
1LEI The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription Deposited 2002-04-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 39–350（312 aa） Fragment：p50 RHR
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions SMALL TUBES；pH 6.5；291 K；PEG 3350, CaCl2, sodium spermine, pH 6.5, SMALL TUBES, temperature 291K
Resolution 2.70 Å R-free 0.284
1NFK STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER Deposited 1995-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 39–363（325 aa）
Chain B 39–363（325 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.340
1OOA CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER Deposited 2003-03-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 39–363（325 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 8000, ethylene glycol, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.45 Å R-free 0.248
1OOA CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER Deposited 2003-03-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 39–363（325 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG 8000, ethylene glycol, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.45 Å R-free 0.248
1U36 Crystal structure of WLAC mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Mutation：Y267W, V310C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.89 Å R-free 0.220
1U3J Crystal structure of MLAV mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Mutation：Y267M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.90 Å R-free 0.222
1U3Y Crystal structure of ILAC mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Mutation：Y267I, V310C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.90 Å R-free 0.223
1U3Z Crystal structure of MLAC mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Mutation：Y267M, V310C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.90 Å R-free 0.235
1U41 Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Chain B 245–350（106 aa） Fragment：dimerization domain
Mutation：A308G Mutation：A308G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.20 Å R-free 0.235
1U41 Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 245–350（106 aa） Fragment：dimerization domain
Chain D 245–350（106 aa） Fragment：dimerization domain
Mutation：A308G Mutation：A308G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.20 Å R-free 0.235
1U42 Crystal structure of MLAM mutant of dimerisation domain of NF-kB p50 transcription factor Deposited 2004-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 245–350（106 aa） Fragment：dimerization domain
Mutation：Y267M, V310M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.317
2I9T Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter Deposited 2006-09-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 39–350（312 aa） Fragment：residues 39-350
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；293 K；8% PEG 5K monomethylether, 200mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60
Resolution 2.80 Å R-free 0.288
2V2T X-ray structure of a NF-kB p50-RelB-DNA complex Deposited 2007-06-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 38–363（326 aa） Fragment：NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT, RESIDUES 38-363
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；5% PEG3350 100 MM NACITRATE 1MM SPERMINE 5MM DTT, pH 7
Resolution 3.05 Å R-free 0.276
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 245–359（115 aa） Fragment：dimerization domain (UNP residues 245-359)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.15 Å R-free 0.280
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 245–359（115 aa） Fragment：dimerization domain (UNP residues 245-359)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.15 Å R-free 0.280
3JV4 Crystal structure of the dimerization domains p50 and RelB Deposited 2009-09-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 245–359（115 aa） Fragment：dimerization domain (UNP residues 245-359)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.15 Å R-free 0.280
8TKL Murine NF-kappaB p50 Rel Homology Region homodimer in complex with a Test 16-mer kappaB-like DNA Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 39–350（312 aa）
Chain B 39–350（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；4% Tacsimate pH 6.0, 12% PEG 3350
Resolution 3.00 Å R-free 0.284
8TKM Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 17-mer kappaB DNA from human interleukin-6 (IL-6) promoter Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 39–350（312 aa）
Chain B 39–350（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Na-Acetate pH 4.9, 16% (w/v) PEG 1500
Resolution 2.80 Å R-free 0.273
8TKN Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 10-mer kappaB DNA from human Neutrophil Gelatinase-associated Lipocalin (NGAL) promoter Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 39–350（312 aa）
Chain B 39–350（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；0.05 M sodium acetate pH 5.4, 20 mM magnesium sulfate, and 4% PEG 3350
Resolution 2.80 Å R-free 0.288
9BOR IkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex at 2.0 Angstrom resolution Deposited 2024-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 245–376（132 aa）
Chain C 245–376（132 aa）
Not recorded HT3 (2R,3S)-heptane-1,2,3-triol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；303 K；20mM acetic acid pH 5.2, 80mM acetic acid pH 5.8, 5.5% PEG 3350, 10mM DTT, 0.5% 1,2,3 heptanetriol
Resolution 2.00 Å R-free 0.208

20 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NFKB1_MOUSE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–312； UniProt 39–350

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1vkx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vkx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vkx
Deposition date deposition_date1997-09-17
Structure title titleCRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA
Keywords keywordsTRANSCRIPTION FACTOR, NF-KB, HETERODIMER, DNA-BINDING, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.63 Å
Radius of gyration Rg (electron density) rg_electron31.14 Å
Forward intensity I(0) i099620600.00
Molecular weight molecular_weight73131.0 kDa
Excluded volume excluded_volume89072 ų
Envelope volume envelope_volume115930 ų
Hydration-shell volume shell_volume32691 ų
Envelope diameter envelope_diameter109.4 Å
Shell Rg shell_rg36.04 Å
Envelope Rg envelope_rg31.30 Å
Shape Rg shape_rg31.18 Å
Total Rg total_rg31.43 Å
Total atoms total_atoms5116
Residues n_residues609
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax103.8 Å
Rg (real space) rg_real30.70 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real9.9620e+07
I(0) uncertainty (real space) i0_real_error1.5930e+06
Rg (reciprocal space) rg_reciprocal30.68 Å
I(0) (reciprocal space) i0_reciprocal99620000.0000
Solution quality estimate total_estimate0.8805
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9 Å
Skewness Skewness skewness0.384
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13090000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.917
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1vkxa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd1vkxa2
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain
Domain ID domain_idd1vkxb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd1vkxb2
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id1vkxA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id1vkxA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1vkxB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id1vkxB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (2)

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9. Files and Curves (10)