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- PDB-1nfk: STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER -

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Basic information

Entry
Database: PDB / ID: 1nfk
TitleSTRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER
Components
  • DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3')
  • PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))
KeywordsTRANSCRIPTION/DNA / NF-KB P50 / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX
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 / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process ...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 / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / MAP3K8 (TPL2)-dependent MAPK1/3 activation / PKMTs methylate histone lysines / NF-kB is activated and signals survival / mammary gland involution / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / Activation of NF-kappaB in B cells / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / antibacterial innate immune response / Downstream TCR signaling / 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 / actinin binding / cellular response to dsRNA / 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 / canonical NF-kappaB signal transduction / Neutrophil degranulation / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cellular response to tumor necrosis factor / transcription coactivator binding / sequence-specific double-stranded DNA binding / positive regulation of inflammatory response / 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
Rel homology domain (RHD), DNA-binding 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 domain (RHD), DNA-binding 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 / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / 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
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsGhosh, G. / Van Duyne, G. / Ghosh, S. / Sigler, P.B.
CitationJournal: 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
DepositionFeb 28, 1995Processing site: NDB
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3')
A: PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))
B: PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))


Theoretical massNumber of molelcules
Total (without water)79,8944
Polymers79,8944
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.200, 132.100, 80.100
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-32-

HOH

21A-446-

HOH

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Components

#1: DNA chain DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3')


Mass: 3349.197 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))


Mass: 36597.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25799
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 52 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlDNA1drop
225 mMHEPES1drop
35 mMdithiothreitol1drop
450 mMammonium chloride1drop
55 mM1dropCaCl2
60.05 mMspermine1drop
70.05 %(w/v)beta-octylglucoside1drop
84 %PEG40001drop
950 mMHEPES1reservoir
1010 mMdithiothreitol1reservoir
11100 mMammonium chloride1reservoir
1210 mM1reservoirCaCl2
130.10 mMspermine1reservoir
140.10 %(w/v)beta-octylglucoside1reservoir
158 %PEG40001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONCHESS A11
SYNCHROTRONCHESS A12
Detector
TypeIDDetector
RIGAKU RAXIS II1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionNum. obs: 30826 / % possible obs: 96 %
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96 % / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementResolution: 2.3→6 Å / σ(F): 3
RfactorNum. reflection
Rfree0.34 -
Rwork0.23 -
obs0.23 28020
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 492 0 951 7479
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2

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