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- PDB-1oy3: CRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1oy3
TitleCRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX
Components
  • Transcription factor p65
  • transcription factor inhibitor I-kappa-B-beta
KeywordsDNA BINDING PROTEIN / 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 / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / canonical NF-kappaB signal transduction / hair follicle development / response to amino acid / neuropeptide signaling pathway / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / antiviral innate immune response / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / liver development / response to progesterone / positive regulation of interleukin-1 beta production / response to ischemia / animal organ morphogenesis / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of extrinsic apoptotic signaling pathway / response to insulin / response to bacterium / protein catabolic process / defense response / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of miRNA transcription / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to nicotine / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of NF-kappaB transcription factor activity / cellular response to tumor necrosis factor / chromatin organization / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / transcription regulator complex / sequence-specific DNA binding / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of cell population proliferation
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMalek, S. / Huang, D.B. / 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
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,8153
Polymers61,8153
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-22 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.620, 54.790, 59.570
Angle α, β, γ (deg.)102.56, 96.07, 91.90
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


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) / Gene: RELA OR NFKB3 / Plasmid: PET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q04207
#2: Protein transcription factor inhibitor I-kappa-B-beta


Mass: 30327.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet29b / 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.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 29193 / % possible obs: 78.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.1
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2 / Num. unique all: 2768 / % possible all: 75

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3Z

1k3z


Resolution: 2.05→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 1459 3.9 %RANDOM
Rwork0.2182 ---
all0.2193 ---
obs0.2193 29193 78.1 %-
Solvent computationBsol: 44.5406 Å2 / ksol: 0.356903 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.13 Å2-0.211 Å2-1.18 Å2
2---3.053 Å20.794 Å2
3---5.183 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 0 248 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it2.6841.5
X-RAY DIFFRACTIONc_mcangle_it3.8612
X-RAY DIFFRACTIONc_scbond_it4.2022
X-RAY DIFFRACTIONc_scangle_it5.5662.5
LS refinement shellResolution: 2.05→2.1 Å
RfactorNum. reflection
Rfree0.296 62
Rwork0.299 -
obs-1093

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