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- PDB-7jfl: Crystal structure of human phosphorylated IRF-3 bound to CBP -

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Basic information

Entry
Database: PDB / ID: 7jfl
TitleCrystal structure of human 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 / MDA-5 signaling pathway / macrophage apoptotic process / 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 ...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 / 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 / IRF3-mediated induction of type I IFN / NFE2L2 regulating MDR associated enzymes / positive regulation of cytokine production involved in inflammatory response / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cGAS/STING signaling pathway / signal transduction involved in regulation of gene expression / mRNA transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / 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 / DNA-binding transcription activator activity / protein acetylation / cytoplasmic pattern recognition receptor signaling pathway / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / cellular response to exogenous dsRNA / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / FOXO-mediated transcription of cell death genes / 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 / antiviral innate immune response / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / TICAM1-dependent activation of IRF3/IRF7 / BMAL1:CLOCK,NPAS2 activates circadian expression / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / SUMOylation of transcription cofactors / lipopolysaccharide-mediated signaling pathway / Activation of gene expression by SREBF (SREBP) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / Transcriptional activation of mitochondrial biogenesis
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 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 20, 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)58,0904
Polymers58,0904
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-43 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.010, 68.030, 55.920
Angle α, β, γ (deg.)90.000, 106.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23770.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.95 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5.0, 0.2 M MgCl2, 5% 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: 1.68→46.93 Å / Num. obs: 48116 / % possible obs: 94.7 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.068 / Net I/σ(I): 6.5
Reflection shellResolution: 1.68→1.7 Å / Redundancy: 3.1 % / Num. unique obs: 2336 / CC1/2: 0.352 / % possible all: 90.6

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Processing

Software
NameVersionClassification
MOSFLM1.18.2_3874data reduction
Aimless0.5.21data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JEM

5jem


Resolution: 1.68→46.93 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 2377 4.94 %
Rwork0.191 45716 -
obs0.1927 48093 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.36 Å2 / Biso mean: 24.4488 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.68→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 0 252 3898
Biso mean---27.77 -
Num. residues----464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.710.36271150.32022563267890
1.71-1.750.31191350.2912585272091
1.75-1.790.31771290.27032611274092
1.79-1.840.28621240.24972656278093
1.84-1.890.29311510.2172617276893
1.89-1.940.21721350.19812684281994
1.94-2.010.22741410.19152698283995
2.01-2.080.24391370.19912703284095
2.08-2.160.21731450.19072690283595
2.16-2.260.21431430.18142709285295
2.26-2.380.23081240.18072725284995
2.38-2.530.23441630.19142723288695
2.53-2.720.22081520.1922709286196
2.72-2.990.23571420.19182700284295
2.99-3.430.18981440.18032761290596
3.43-4.320.18141440.15782757290196
4.32-46.930.21931530.18412825297897
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)
12.6296-1.38680.44640.95380.75953.87650.0218-0.04310.16350.27020.2073-0.5577-0.19170.1525-0.11670.1261-0.03970.01590.15730.02280.105-15.865912.957811.6445
21.77721.05980.42685.64951.48422.99530.01580.0973-0.0464-0.40340.0853-0.6713-0.23870.2382-0.14160.1552-0.00740.04910.2118-0.0290.256-10.866813.14936.3333
31.90031.87550.83566.76281.32652.8502-0.00180.0888-0.1224-0.32080.1105-0.69510.03740.118-0.2030.13110.00850.02990.1581-0.01130.1663-13.78120.5674-0.3952
43.0366-2.0115-2.11686.33891.94663.34840.1264-0.00470.2749-0.2870.1406-0.3952-0.35070.0769-0.25130.217-0.00940.00690.12450.02280.1536-19.850422.25984.3037
52.5273-1.3691.33545.5578-1.73344.114-0.0469-0.03540.0091-0.156-0.00550.0802-0.3524-0.01670.00980.1529-0.0082-0.01990.1209-0.03480.1232-27.024813.7644.3398
62.17890.462-3.82771.1057-1.55266.8636-0.04610.05870.0139-0.00660.05930.09860.0123-0.2863-0.02830.12120.0047-0.01930.1564-0.0180.1631-29.634222.032621.2429
71.4577-1.9073-1.36364.7919-0.08954.204-0.03730.1137-0.1674-0.3583-0.010.4220.2723-0.47750.04960.1348-0.0336-0.0280.1762-0.00690.1321-27.59054.63275.4607
80.5982-0.2997-1.27482.47042.50523.91740.04520.00710.0486-0.105-0.08680.0593-0.0814-0.04320.0470.12990.0084-0.02770.14690.00740.1554-20.764315.976421.2146
93.68912.10551.04349.18032.26571.6608-0.14860.1371-0.3773-0.19170.06570.03020.0795-0.07630.14870.13830.02470.04040.18490.00520.1758-36.34335.897432.7645
102.91922.13212.83384.9201-0.16084.2673-0.1087-0.98691.01030.7151-0.8485-1.28950.04470.40650.66730.3458-0.0567-0.20190.58680.09540.7495-15.424124.346835.0887
115.2138-4.1511-5.04668.55035.39875.2433-0.3006-1.6016-0.92880.15330.03341.72070.4095-0.71330.29210.26140.0468-0.05010.79770.04010.6339-12.438316.674528.5938
125.6802-3.4528-2.76496.76353.3176.63310.0821-0.37150.7420.34630.3215-0.9153-0.22930.5956-0.36270.1933-0.063-0.0060.1985-0.04770.2227-13.960927.206222.8317
136.292.7462-3.17513.3795-3.33483.58930.2883-0.52750.28670.807-0.1839-0.0061-0.77770.0765-0.0920.26740.0045-0.0040.177-0.07530.2217-24.971529.328931.8141
142.37170.7058-0.40920.39420.56082.4634-0.1058-0.1375-0.39170.1950.1985-0.20560.43610.1274-0.11630.15250.0118-0.01530.14890.03680.1665-19.2502-14.540126.5098
153.6122-0.6193-1.15895.19581.51911.4672-0.0718-0.2159-0.09680.4417-0.04630.02380.23860.16890.1710.1583-0.0027-0.04030.1694-0.01260.1353-18.297-12.1132.5248
163.2537-4.03070.38127.2429-1.47991.0415-0.0702-0.08830.24750.47040.0753-0.3415-0.06160.0553-0.01770.1476-0.0149-0.01940.1647-0.03250.1063-24.48141.544536.3498
171.38670.72530.4366.62962.8574.93450.0285-0.0417-0.04790.23670.0976-0.01690.248-0.0401-0.11460.1654-0.00750.0010.11680.03060.139-26.9306-20.20529.1747
185.14941.9779-1.51154.6716-1.96632.8271-0.1390.28390.0362-0.12340.06060.21010.0734-0.23570.00920.10470.0073-0.00140.1333-0.02610.1787-31.8098-8.949523.0321
196.26121.4066-0.97416.4915-2.40166.8860.0587-0.3966-0.53280.3979-0.15510.23470.28960.08110.07610.1336-0.01140.03670.1479-0.01080.1912-35.5405-17.68430.1333
201.31360.6641-3.28971.9114-0.8869.0035-0.0840.1479-0.0138-0.21970.03730.052-0.1277-0.38760.02680.09370.0056-0.03060.145-0.02730.1297-26.1173-20.02399.5802
211.03471.3621-0.61833.04080.5143.86510.03820.13710.18420.0588-0.02330.4706-0.2621-0.4119-0.0280.09050.0283-0.010.15430.00230.1793-33.1532-2.644124.1837
220.7065-1.4084-1.8822.77863.69695.78520.08410.01290.05950.00640.008-0.08660.0048-0.0037-0.12060.1171-0.0054-0.00890.13620.01110.1665-18.6269-13.84814.4568
236.131-2.09980.06135.03552.08411.3543-0.1343-0.05110.04670.00150.05360.4226-0.1386-0.24990.05110.2491-0.0322-0.04190.1972-0.02690.1103-25.7033-3.9203-3.6671
242.5850.47220.49238.78225.74043.7908-0.02341.40730.3249-1.1302-0.1456-0.6114-0.55180.3804-0.0340.4516-0.0505-0.0420.83520.06790.5093-7.0648-19.93599.6832
254.69196.08545.13587.82166.62075.62120.27640.2021-0.49950.37460.1066-0.62460.56380.5284-0.39780.16720.0168-0.01770.1787-0.01170.1959-11.5985-24.475616.9023
265.25950.6098-1.68233.1912-3.0083.21660.00750.4094-0.258-0.3926-0.0961-0.2163-0.0193-0.07880.00570.27250.0199-0.01320.177-0.07120.2045-17.0367-27.65934.0775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 199 through 212 )A199 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 240 )A213 - 240
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 267 )A241 - 267
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 285 )A268 - 285
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 316 )A286 - 316
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 342 )A317 - 342
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 363 )A343 - 363
8X-RAY DIFFRACTION8chain 'A' and (resid 364 through 381 )A364 - 381
9X-RAY DIFFRACTION9chain 'A' and (resid 382 through 396 )A382 - 396
10X-RAY DIFFRACTION10chain 'C' and (resid 2069 through 2073 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 2074 through 2079 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 2080 through 2092 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 2093 through 2104 )C0
14X-RAY DIFFRACTION14chain 'B' and (resid 195 through 212 )B195 - 212
15X-RAY DIFFRACTION15chain 'B' and (resid 213 through 240 )B213 - 240
16X-RAY DIFFRACTION16chain 'B' and (resid 241 through 267 )B241 - 267
17X-RAY DIFFRACTION17chain 'B' and (resid 268 through 285 )B268 - 285
18X-RAY DIFFRACTION18chain 'B' and (resid 286 through 306 )B286 - 306
19X-RAY DIFFRACTION19chain 'B' and (resid 307 through 316 )B307 - 316
20X-RAY DIFFRACTION20chain 'B' and (resid 317 through 342 )B317 - 342
21X-RAY DIFFRACTION21chain 'B' and (resid 343 through 363 )B343 - 363
22X-RAY DIFFRACTION22chain 'B' and (resid 364 through 381 )B364 - 381
23X-RAY DIFFRACTION23chain 'B' and (resid 382 through 396 )B382 - 396
24X-RAY DIFFRACTION24chain 'D' and (resid 2066 through 2079 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 2080 through 2092 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 2093 through 2103 )D0

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