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- PDB-5oen: Crystal Structure of STAT2 in complex with IRF9 -

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Basic information

Entry
Database: PDB / ID: 5oen
TitleCrystal Structure of STAT2 in complex with IRF9
Components
  • Interferon regulatory factor 9
  • Signal transducer and activator of transcription
KeywordsTRANSCRIPTION / STAT2 / IRF9
Function / homology
Function and homology information


ISGF3 complex / Interferon alpha/beta signaling / immune system process / sequence-specific double-stranded 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 / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II ...ISGF3 complex / Interferon alpha/beta signaling / immune system process / sequence-specific double-stranded 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 / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / 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. / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction ...Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / 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. / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / 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 / SMAD/FHA domain superfamily / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Signal transducer and activator of transcription / Interferon regulatory factor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.919 Å
AuthorsRengachari, S. / Panne, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function.
Authors: Rengachari, S. / Groiss, S. / Devos, J.M. / Caron, E. / Grandvaux, N. / Panne, D.
History
DepositionJul 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor 9
B: Signal transducer and activator of transcription


Theoretical massNumber of molelcules
Total (without water)39,3392
Polymers39,3392
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-6 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.602, 124.037, 51.029
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon regulatory factor 9 / IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon- ...IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon-stimulated gene factor 3 gamma / ISGF-3 gamma / Transcriptional regulator ISGF3 subunit gamma


Mass: 19100.721 Da / Num. of mol.: 1 / Fragment: UNP residues 206-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf9, Isgf3g
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q61179
#2: Protein Signal transducer and activator of transcription


Mass: 20238.412 Da / Num. of mol.: 1 / Fragment: UNP residues 141-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stat2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q3UDU1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium formate and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.919→39.389 Å / Num. obs: 7970 / % possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 5.9
Reflection shellResolution: 2.919→2.93 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.898 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BF5

1bf5


Resolution: 2.919→32.12 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.307 761 10.19 %RANDOM
Rwork0.255 ---
obs0.26 7469 88.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 2.919→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 19 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022754
X-RAY DIFFRACTIONf_angle_d0.4633725
X-RAY DIFFRACTIONf_dihedral_angle_d13.021689
X-RAY DIFFRACTIONf_chiral_restr0.035415
X-RAY DIFFRACTIONf_plane_restr0.003486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9003-3.1240.37551240.29821123X-RAY DIFFRACTION74
3.124-3.43810.33431610.28471268X-RAY DIFFRACTION85
3.4381-3.93480.33671400.26211408X-RAY DIFFRACTION93
3.9348-4.95450.27571870.22791437X-RAY DIFFRACTION96
4.9545-32.11790.28351490.24681472X-RAY DIFFRACTION95

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