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- PDB-3a77: The crystal structure of phosphorylated IRF-3 -

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Basic information

Entry
Database: PDB / ID: 3a77
TitleThe crystal structure of phosphorylated IRF-3
ComponentsInterferon regulatory factor 3IRF3
KeywordsTRANSCRIPTION / phosphorylated protein / Activator / Antiviral defense / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / TRAF6 mediated IRF7 activation ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / DNA-binding transcription activator activity / immune system process / cellular response to exogenous dsRNA / type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / apoptotic process / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Interferon regulatory factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakahasi, K. / Horiuchi, M. / Noda, N.N. / Inagaki, F.
CitationJournal: Genes Cells / Year: 2010
Title: Ser386 phosphorylation of transcription factor IRF-3 induces dimerization and association with CBP/p300 without overall conformational change.
Authors: Takahasi, K. / Horiuchi, M. / Fujii, K. / Nakamura, S. / Noda, N.N. / Yoneyama, M. / Fujita, T. / Inagaki, F.
History
DepositionSep 17, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 3
B: Interferon regulatory factor 3
C: Interferon regulatory factor 3
D: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,42210
Polymers107,8294
Non-polymers5936
Water18,1411007
1
A: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1363
Polymers26,9571
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0762
Polymers26,9571
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1363
Polymers26,9571
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Interferon regulatory factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0762
Polymers26,9571
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.469, 102.459, 68.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Interferon regulatory factor 3 / IRF3 / IRF-3


Mass: 26957.332 Da / Num. of mol.: 4 / Fragment: UNP residues 189-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Plasmid: pPRO Ex HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q14653
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% MPD, 50mM sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 107284 / Num. obs: 107284 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.32 / Num. unique all: 10491 / % possible all: 98.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J2F

1j2f


Resolution: 1.8→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 10499 -RANDOM
Rwork0.1937 ---
all0.197 104991 --
obs0.197 104991 87.7 %-
Displacement parametersBiso mean: 0.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.179 Å20 Å20 Å2
2---0.675 Å20 Å2
3---0.496 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7281 0 40 1007 8328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 1.8→1.81 Å
RfactorNum. reflection
Rfree0.256 214
Rwork0.2294 -
obs-1651

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