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- PDB-1vkx: CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO TH... -

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Basic information

Entry
Database: PDB / ID: 1vkx
TitleCRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA
Components
  • DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3')
  • PROTEIN (NF-KAPPA B P50 SUBUNIT)
  • PROTEIN (NF-KAPPA B P65 SUBUNIT)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / NF-KB / HETERODIMER / DNA-BINDING / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


SUMOylation of immune response proteins / 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 ...SUMOylation of immune response proteins / 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 / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / mammary gland involution / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / antibacterial innate immune response / prolactin signaling pathway / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / response to cobalamin / cellular response to peptidoglycan / positive regulation of lipid storage / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / negative regulation of cytokine production / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / response to cAMP / canonical NF-kappaB signal transduction / positive regulation of cholesterol efflux / hair follicle development / NF-kappaB binding / positive regulation of transcription initiation by RNA polymerase II / lymph node development / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / JNK cascade / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / negative regulation of insulin receptor signaling pathway / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / defense response / response to insulin / negative regulation of protein catabolic process
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 / 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 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
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 2.9 Å
AuthorsChen, F. / Huang, D.B. / Ghosh, G.
Citation
Journal: Nature / Year: 1998
Title: Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA.
Authors: Chen, F.E. / Huang, D.B. / Chen, Y.Q. / Ghosh, G.
#1: Journal: Nature / Year: 1995
Title: Structure of NF-Kb p50 Homodimer Bound to a Kb Site
Authors: Ghosh, G. / Duyne, G.V. / Ghosh, S. / Sigler, P.B.
History
DepositionSep 17, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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*GP*AP*CP*TP*TP*TP*CP*C)-3')
D: DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3')
A: PROTEIN (NF-KAPPA B P65 SUBUNIT)
B: PROTEIN (NF-KAPPA B P50 SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)73,2354
Polymers73,2354
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.610, 106.610, 206.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

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


Mass: 3669.389 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65
#2: DNA chain DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3') / IMMUNOGLOBULIN KAPPA B DNA


Mass: 3656.407 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65
#3: Protein PROTEIN (NF-KAPPA B P65 SUBUNIT)


Mass: 30984.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q04207
#4: Protein PROTEIN (NF-KAPPA B P50 SUBUNIT)


Mass: 34924.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P25799
Has protein modificationY

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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: 3.99 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2CACL211
3BETA-OCTYL-GLUCOSIDE11
4SPERMINE11
5DITHIOTHREITOL11
6PEG 335011
7PEG 335012
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 mMsodium acetate1reservoir
3100 mM1reservoirCaCl2
48 %PEG33501reservoir
510 mMdithiothreitol1reservoir
61
71

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 26430 / % possible obs: 97 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.45 / % possible all: 88
Reflection
*PLUS
Num. measured all: 88449
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: ONE MONOMER OF P50/DNA COMPLEX AND ONE MONO OF P65/DNA COMPLEX

Resolution: 2.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.32 978 5 %
Rwork0.208 --
obs0.208 19562 -
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 486 0 0 5116
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_deg1.97
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.86
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.86

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