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- PDB-1k3z: X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex -

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Basic information

Entry
Database: PDB / ID: 1k3z
TitleX-ray crystal structure of the IkBb/NF-kB p65 homodimer complex
Components
  • Transcription factor p65
  • transcription factor inhibitor I-kappa-B-beta
KeywordsTRANSCRIPTION / protein-protein complex / transcription factors / nuclear localization
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 / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / 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 / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / 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 / prolactin signaling pathway / Downstream TCR signaling / 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 / 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 / actinin binding / non-canonical NF-kappaB signal transduction / response to UV-B / regulation of canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / 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 / 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 lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / canonical NF-kappaB signal transduction / response to cAMP / hair follicle development / NF-kappaB binding / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / 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 / chromatin DNA binding / positive regulation of interleukin-6 production / cellular response to nicotine / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / chromatin organization / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity
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 / Ankyrin repeat-containing domain / IPT domain / p53-like transcription factor, DNA-binding / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcription factor p65 / NF-kappa-B inhibitor beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShiva, M. / Huang, D.B. / Chen, Y. / Huxford, T. / Ghosh, S. / Ghosh, G.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: X-ray crystal structure of an IkappaBbeta x NF-kappaB p65 homodimer complex.
Authors: Malek, S. / Huang, D.B. / Huxford, T. / Ghosh, S. / Ghosh, G.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor p65
B: Transcription factor p65
D: transcription factor inhibitor I-kappa-B-beta


Theoretical massNumber of molelcules
Total (without water)62,0253
Polymers62,0253
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-14 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 48.920, 59.470
Angle α, β, γ (deg.)95.17, 91.80, 105.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / NF-KB P65


Mass: 15743.802 Da / Num. of mol.: 2 / Fragment: p65 dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q04207
#2: Protein transcription factor inhibitor I-kappa-B-beta / IKBB


Mass: 30537.604 Da / Num. of mol.: 1 / Mutation: S312E, S313E, S314E, S316E, S318E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q60778
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-10 %PEG80001reservoir
2sodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 15, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 16126 / Num. obs: 13724 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3 / Num. unique all: 1430 / % possible all: 72
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 16126 / % possible obs: 93 % / Num. measured all: 110726
Reflection shell
*PLUS
% possible obs: 72 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IkBalpha/p65dd (pdb entry 1ikn)

1ikn


Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 669 4.8 %random
Rwork0.181 ---
all-16126 --
obs-13724 80 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 0 99 3769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.32
LS refinement shellResolution: 2.5→2.57 Å
RfactorNum. reflection% reflection
Rfree0.389 28 4.5 %
Rwork0.244 --
obs-616 -
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 15382 / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.34

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