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- PDB-1bfs: STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE -

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Basic information

Entry
Database: PDB / ID: 1bfs
TitleSTRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE
ComponentsNUCLEAR FACTOR NF-KAPPA-B P50
KeywordsTRANSCRIPTION FACTOR / NF-KB / DIMERIZATION DOMAIN
Function / homology
Function and homology information


cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation ...cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / mammary gland involution / Activation of NF-kappaB in B cells / cellular response to carbohydrate stimulus / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / Downstream TCR signaling / antibacterial innate immune response / CD209 (DC-SIGN) signaling / cellular response to peptide / negative regulation of interleukin-12 production / positive regulation of lipid storage / signal transduction involved in regulation of gene expression / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / positive regulation of miRNA metabolic process / negative regulation of cytokine production / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to angiotensin / positive regulation of cholesterol efflux / cellular response to interleukin-1 / lymph node development / positive regulation of transcription initiation by RNA polymerase II / cis-regulatory region sequence-specific DNA binding / JNK cascade / response to muscle stretch / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / Neutrophil degranulation / canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / tumor necrosis factor-mediated signaling pathway / B cell receptor signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / protein sequestering activity / cellular response to mechanical stimulus / cellular response to virus / cellular response to nicotine / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / transcription coactivator binding / positive regulation of inflammatory response / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to lipopolysaccharide / response to oxidative stress / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear factor NF-kappa-B, p105 subunit / : / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain ...Nuclear factor NF-kappa-B, p105 subunit / : / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Ankyrin repeat / Death-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, D.B. / Huxford, T. / Chen, Y.Q. / Ghosh, G.
Citation
Journal: Structure / Year: 1997
Title: The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits.
Authors: Huang, D.B. / Huxford, T. / Chen, Y.Q. / Ghosh, G.
#1: Journal: Nature / Year: 1995
Title: Structure of NF-Kappa B p50 Homodimer Bound to a Kappa B Site
Authors: Ghosh, G. / Van Duyne, G. / Ghosh, S. / Sigler, P.B.
History
DepositionSep 12, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR FACTOR NF-KAPPA-B P50


Theoretical massNumber of molelcules
Total (without water)12,2571
Polymers12,2571
Non-polymers00
Water1,29772
1
A: NUCLEAR FACTOR NF-KAPPA-B P50

A: NUCLEAR FACTOR NF-KAPPA-B P50


Theoretical massNumber of molelcules
Total (without water)24,5142
Polymers24,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)62.330, 62.330, 65.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NUCLEAR FACTOR NF-KAPPA-B P50


Mass: 12256.831 Da / Num. of mol.: 1 / Fragment: DIMERIZATION DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25799
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.08 Mcacodylate1reservoir
20.16 Mammonium sulfate1reservoir
330 %PEG80001reservoir
40.04 Mcacodylate1drop
50.08 Mammonium sulfate1drop
615 %PEG80001drop
77 mg/mlp50dd1drop

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 7896 / % possible obs: 98 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.1 / % possible all: 98.6

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.287 561 10 %
Rwork0.183 --
obs0.183 5613 70 %
Displacement parametersBiso mean: 28.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 78 942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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