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- PDB-1bft: STRUCTURE OF NF-KB P65 HOMODIMER BOUND TO A KB SITE -

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Basic information

Entry
Database: PDB / ID: 1bft
TitleSTRUCTURE OF NF-KB P65 HOMODIMER BOUND TO A KB SITE
ComponentsNUCLEAR FACTOR NF-KAPPA-B P65
KeywordsTRANSCRIPTION FACTOR / NF-KB / DIMERIZATION DOMAIN
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / positive regulation of Schwann cell differentiation / PKMTs methylate histone lysines / TAK1-dependent IKK and NF-kappa-B activation ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / positive regulation of Schwann cell differentiation / 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 / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / positive regulation of chondrocyte differentiation / prolactin signaling pathway / NF-kappaB p50/p65 complex / Downstream TCR signaling / toll-like receptor TLR6:TLR2 signaling pathway / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / positive regulation of T cell receptor signaling pathway / defense response to tumor cell / signal transduction involved in regulation of gene expression / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / response to UV-B / positive regulation of miRNA metabolic process / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / vascular endothelial growth factor signaling pathway / NF-kappaB complex / positive regulation of amyloid-beta formation / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / cellular response to angiotensin / general transcription initiation factor binding / hair follicle development / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / peptide binding / positive regulation of interleukin-12 production / canonical NF-kappaB signal transduction / negative regulation of insulin receptor signaling pathway / response to cytokine / negative regulation of cytokine production involved in inflammatory response / negative regulation of miRNA transcription / response to interleukin-1 / antiviral innate immune response / negative regulation of angiogenesis / animal organ morphogenesis / tumor necrosis factor-mediated signaling pathway / : / positive regulation of interleukin-1 beta production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / neuropeptide signaling pathway / liver development / defense response / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to nicotine / positive regulation of miRNA transcription / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / chromatin organization / cellular response to lipopolysaccharide / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Transcription factor RelA (p65) / 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. ...Transcription factor RelA (p65) / 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 / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Feb 26, 2025Group: Structure summary / Category: pdbx_entry_details / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR FACTOR NF-KAPPA-B P65
B: NUCLEAR FACTOR NF-KAPPA-B P65


Theoretical massNumber of molelcules
Total (without water)22,9482
Polymers22,9482
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 74.490, 105.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NUCLEAR FACTOR NF-KAPPA-B P65


Mass: 11473.935 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q04207
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %PEG33501reservoir
2100 mMsodium cacodylate1reservoir
30.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 12401 / % possible obs: 84 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIMERIZATION DOMAINS OF P50RHR/DNA COMPLEX

Resolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.294 456 5 %
Rwork0.204 --
obs0.204 9124 -
Displacement parametersBiso mean: 16.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 0 88 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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