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- PDB-1zoq: IRF3-CBP complex -

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Basic information

Entry
Database: PDB / ID: 1zoq
TitleIRF3-CBP complex
Components
  • CREB-binding protein
  • Interferon regulatory factor 3
Keywordstranscription/transferase / transcription regulation / transferase / transcription-transferase COMPLEX
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / peptide lactyltransferase (CoA-dependent) activity / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / peptide lactyltransferase (CoA-dependent) activity / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / positive regulation of cytokine production involved in inflammatory response / NFE2L2 regulates pentose phosphate pathway genes / positive regulation of type I interferon-mediated signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cGAS/STING signaling pathway / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / mRNA transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / DNA-binding transcription activator activity / embryonic digit morphogenesis / cytoplasmic pattern recognition receptor signaling pathway / immune system process / homeostatic process / type I interferon-mediated signaling pathway / protein acetylation / Notch-HLH transcription pathway / cellular response to exogenous dsRNA / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / antiviral innate immune response / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / positive regulation of type I interferon production / Attenuation phase / positive regulation of interferon-alpha production / regulation of cellular response to heat / histone acetyltransferase activity / lipopolysaccharide-mediated signaling pathway / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / TICAM1-dependent activation of IRF3/IRF7 / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Evasion by RSV of host interferon responses / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / cellular response to virus / ISG15 antiviral mechanism / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis
Similarity search - Function
Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor ...Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / Tumour Suppressor Smad4 / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SMAD/FHA domain superfamily / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon regulatory factor 3 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsQin, B. / Lin, K.
CitationJournal: Structure / Year: 2005
Title: Crystal structure of IRF-3 in complex with CBP.
Authors: Qin, B.Y. / Liu, C. / Srinath, H. / Lam, S.S. / Correia, J.J. / Derynck, R. / Lin, K.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Interferon regulatory factor 3
C: CREB-binding protein
B: Interferon regulatory factor 3
D: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)52,8484
Polymers52,8484
Non-polymers00
Water7,530418
1
A: Interferon regulatory factor 3
C: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)26,4242
Polymers26,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area12530 Å2
MethodPISA
2
B: Interferon regulatory factor 3
D: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)26,4242
Polymers26,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.694, 81.694, 242.096
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Interferon regulatory factor 3 / IRF-3


Mass: 21150.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#2: Protein/peptide CREB-binding protein


Mass: 5274.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 4.41 Å3/Da / Density % sol: 72.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 0.15 M Mg acetate, 5% (v/v) PEG 4000, 50 mM Na HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.36→28.7 Å / Num. all: 35821 / Num. obs: 31570

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Processing

Software
NameVersionClassification
CNS1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→28.7 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The distance between the C-N atoms in residues (B GLU 232 ) and (B VAL 233 ) is 4.75.
RfactorNum. reflectionSelection details
Rfree0.226 1108 0.214
Rwork0.214 --
all0.214 36950 -
obs0.214 31386 -
Refinement stepCycle: LAST / Resolution: 2.37→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 0 418 4138

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