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- PDB-7jfm: Crystal structure of mouse phosphorylated IRF-3 bound to CBP -

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Basic information

Entry
Database: PDB / ID: 7jfm
TitleCrystal structure of mouse phosphorylated IRF-3 bound to CBP
Components
  • CREB-binding protein
  • Interferon regulatory factor 3
KeywordsIMMUNE SYSTEM / transcription factor / phosphorylation / innate immunity
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Negative regulators of DDX58/IFIH1 signaling / TRAF6 mediated IRF7 activation / ISG15 antiviral mechanism / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...IRF3 mediated activation of type 1 IFN / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / IRF3-mediated induction of type I IFN / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Negative regulators of DDX58/IFIH1 signaling / TRAF6 mediated IRF7 activation / ISG15 antiviral mechanism / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of innate immune responses to cytosolic DNA / programmed necrotic cell death / peptide lactyltransferase (CoA-dependent) activity / TRIF-dependent toll-like receptor signaling pathway / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of transcription by RNA polymerase I / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / toll-like receptor 4 signaling pathway / protein-lysine-acetyltransferase activity / type I interferon-mediated signaling pathway / embryonic digit morphogenesis / protein acetylation / cytoplasmic pattern recognition receptor signaling pathway / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / histone acetyltransferase activity / FOXO-mediated transcription of cell death genes / response to exogenous dsRNA / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of interferon-alpha production / histone acetyltransferase complex / immune system process / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / cellular response to nutrient levels / Attenuation phase / positive regulation of double-strand break repair via homologous recombination / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / regulation of cellular response to heat / histone acetyltransferase / : / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of interferon-beta production / SUMOylation of transcription cofactors / lipopolysaccharide-mediated signaling pathway / Activation of gene expression by SREBF (SREBP) / positive regulation of cytokine production / response to bacterium / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding
Similarity search - Function
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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily ...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 / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / 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 / : / Histone acetyltransferase p300-like, PHD domain / 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 (BrD) 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
Similarity search - Domain/homology
Interferon regulatory factor 3 / CREB-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsLi, P. / Jing, T. / Zhao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145287 United States
CitationJournal: J Immunol. / Year: 2020
Title: The Structural Basis of IRF-3 Activation upon Phosphorylation.
Authors: Jing, T. / Zhao, B. / Xu, P. / Gao, X. / Chi, L. / Han, H. / Sankaran, B. / Li, P.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)57,8504
Polymers57,8504
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-42 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.801, 118.801, 72.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

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


Mass: 23650.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70671
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium citrate tribasic at pH 7.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→51.44 Å / Num. obs: 28422 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.027 / Net I/σ(I): 12.6
Reflection shellResolution: 2.23→2.3 Å / Num. unique obs: 2601 / CC1/2: 0.382

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JEM

5jem


Resolution: 2.23→51.44 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1408 4.96 %
Rwork0.2313 26981 -
obs0.2324 28389 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.32 Å2 / Biso mean: 91.163 Å2 / Biso min: 45.97 Å2
Refinement stepCycle: final / Resolution: 2.23→51.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 0 14 3716
Biso mean---67.86 -
Num. residues----468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.310.40851130.378527162829100
2.31-2.40.39941300.34726902820100
2.4-2.510.41241580.357326722830100
2.51-2.640.37871640.317526672831100
2.64-2.810.2981510.322826522803100
2.81-3.030.30971510.293127062857100
3.03-3.330.2891110.266827072818100
3.33-3.810.25021390.224827212860100
3.81-4.80.21691650.201426982863100
4.81-51.440.21211260.19112752287899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.76831.181-2.40135.0234-3.28646.73120.25210.70950.0704-0.5398-0.27330.02420.00650.03290.0250.43330.0518-0.01230.6985-0.19950.545344.5094-5.6798-26.5271
23.1570.54230.36771.8789-1.57642.23310.29790.4180.64330.34420.03740.2665-0.5388-0.1001-0.32160.47130.05680.14620.4765-0.07930.697939.01546.929-15.3591
35.1053-2.7033.71351.4863-1.9542.6999-0.57150.99161.72210.0946-0.527-1.0306-0.96761.02211.03050.9445-0.044-0.03781.32780.24371.472757.302824.7139-18.5545
46.9065-2.31271.05122.79551.44051.7456-0.3280.5120.53350.1904-0.0514-0.6996-0.42680.22650.32290.9203-0.1042-0.08970.94310.13970.955559.848213.318-13.248
54.1199-3.97613.11035.247-1.80363.39170.20181.81410.369-0.7873-1.0889-0.4858-0.07251.21140.50540.8274-0.01050.17121.09540.11011.132755.446515.9534-24.8982
68.6426-3.9003-0.29224.67311.62767.5134-0.44640.16842.2650.26680.6682-0.7732-1.10490.59720.19441.1531-0.0536-0.0810.59750.08621.395546.734926.2199-19.2984
75.52371.275-2.11325.6826-1.70846.26160.1075-0.5131-0.16070.24340.1024-1.52350.07391.62240.12040.58870.2201-0.13930.9755-0.24760.712248.588-5.65961.511
86.448-1.5138-1.11932.1487-3.5678.38750.4352-1.39730.03841.638-0.4991-1.41020.26611.87590.0190.92990.1434-0.31541.90620.00860.624851.24-4.812813.1392
96.33950.2312-1.05436.4149-2.55617.9680.2691-1.15440.67961.31410.1435-0.668-0.79170.9767-0.33840.8245-0.1778-0.01350.9716-0.39450.818248.55467.36986.1385
107.09331.709-1.91185.407-1.96.66540.479-1.7054-0.66271.1427-0.2596-0.75611.09190.98910.00340.96530.2845-0.16641.04910.00280.532541.8887-9.894315.0253
118.10360.5926-0.77954.7871-2.36725.76230.4062-0.1394-0.58450.593-0.44390.0144-0.15180.3205-0.30420.7224-0.0685-0.01360.631-0.18480.631935.2123-4.81123.7269
128.9435-3.0824-2.73769.7027-2.11171.9232-0.5698-1.8934-0.02371.94770.9177-0.32040.21760.5698-0.21660.94620.10860.03770.72670.00250.54734.3313-9.227413.9728
134.13630.0268-2.61348.2056-0.93461.6502-0.6587-0.1175-1.0685-0.2837-0.0480.33091.1399-0.07210.29170.93250.11030.02770.343-0.04370.832135.6646-19.69720.5244
143.4464-0.7864-2.80816.31441.0258.73220.51830.04540.43940.06170.38530.1212-0.9376-0.1382-0.79230.5232-0.05550.11110.5321-0.060.56633.26512.3705-0.9712
151.3644-1.4184-1.9123.02251.62536.2562-0.4469-0.1476-0.8171-0.39070.6374-0.26911.3986-0.288-0.010.8768-0.13040.0530.4674-0.14610.795239.1661-18.2315-10.5774
166.5316-1.9912-2.78464.7604-4.02136.8584-0.18660.0278-1.34384.21850.6365-3.7119-1.8272-0.1783-0.26161.78730.1063-0.49591.10260.1821.906653.6115-29.8809-3.221
174.8094-5.2379-3.81536.59943.61453.3669-1.1962-2.1454-1.4171-0.44520.2376-0.85821.972.84750.73711.5350.64350.15451.63730.14820.92849.9601-26.91316.4837
180.6005-0.14820.08132.5264-0.520.37190.1282-0.0809-0.3709-0.51830.18680.44340.1212-0.13740.22092.92310.48240.2570.16160.44351.64640.391-36.1641-1.702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 191 through 310 )A191 - 310
2X-RAY DIFFRACTION2chain 'A' and (resid 311 through 388 )A311 - 388
3X-RAY DIFFRACTION3chain 'C' and (resid 2066 through 2070 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 2071 through 2079 )C0
5X-RAY DIFFRACTION5chain 'C' and (resid 2080 through 2091 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 2092 through 2104 )C0
7X-RAY DIFFRACTION7chain 'B' and (resid 195 through 214 )B195 - 214
8X-RAY DIFFRACTION8chain 'B' and (resid 215 through 227 )B215 - 227
9X-RAY DIFFRACTION9chain 'B' and (resid 228 through 260 )B228 - 260
10X-RAY DIFFRACTION10chain 'B' and (resid 261 through 278 )B261 - 278
11X-RAY DIFFRACTION11chain 'B' and (resid 279 through 299 )B279 - 299
12X-RAY DIFFRACTION12chain 'B' and (resid 300 through 314 )B300 - 314
13X-RAY DIFFRACTION13chain 'B' and (resid 315 through 341 )B315 - 341
14X-RAY DIFFRACTION14chain 'B' and (resid 342 through 355 )B342 - 355
15X-RAY DIFFRACTION15chain 'B' and (resid 356 through 390 )B356 - 390
16X-RAY DIFFRACTION16chain 'D' and (resid 2067 through 2079 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 2080 through 2092 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 2093 through 2106 )D0

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