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- PDB-8d3f: Crystal structure of human STAT1 in complex with the repeat regio... -

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Basic information

Entry
Database: PDB / ID: 8d3f
TitleCrystal structure of human STAT1 in complex with the repeat region from Toxoplasma protein TgIST
ComponentsSignal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST
KeywordsTRANSCRIPTION / Signal transduction / Transcriptional activation / Pathogen effector / Interferon signaling
Function / homology
Function and homology information


metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding ...metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / tumor necrosis factor receptor binding / Interleukin-27 signaling / Interleukin-35 Signalling / cell surface receptor signaling pathway via STAT / blood circulation / positive regulation of mesenchymal cell proliferation / NOTCH3 Intracellular Domain Regulates Transcription / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / histone acetyltransferase binding / negative regulation of endothelial cell proliferation / ubiquitin-like protein ligase binding / Regulation of IFNA/IFNB signaling / positive regulation of interferon-alpha production / response to cAMP / cell surface receptor signaling pathway via JAK-STAT / response to type II interferon / type II interferon-mediated signaling pathway / response to mechanical stimulus / Regulation of IFNG signaling / Growth hormone receptor signaling / RNA polymerase II core promoter sequence-specific DNA binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / cellular response to interferon-beta / Signaling by CSF3 (G-CSF) / positive regulation of defense response to virus by host / response to cytokine / negative regulation of canonical NF-kappaB signal transduction / response to nutrient / positive regulation of smooth muscle cell proliferation / Downstream signal transduction / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / transcription corepressor binding / tumor necrosis factor-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / response to hydrogen peroxide / Signaling by SCF-KIT / defense response / response to peptide hormone / Inactivation of CSF3 (G-CSF) signaling / PKR-mediated signaling / cellular response to type II interferon / ISG15 antiviral mechanism / transcription coactivator binding / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / Interferon gamma signaling / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / histone binding / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / axon / dendrite / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm
Similarity search - Function
Signal transducer and activation of transcription 1, TAZ2 binding domain, C-terminal / STAT1, SH2 domain / STAT1, C-terminal domain superfamily / STAT1 TAZ2 binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : ...Signal transducer and activation of transcription 1, TAZ2 binding domain, C-terminal / STAT1, SH2 domain / STAT1, C-terminal domain superfamily / STAT1 TAZ2 binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Inhibitor of STAT1-dependent transcription TgIST / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Toxoplasma gondii GT1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsHuang, Z. / Liu, H. / Nix, J.C. / Amarasinghe, G.K. / Sibley, L.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118426 United States
CitationJournal: Nat Commun / Year: 2022
Title: The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment.
Authors: Huang, Z. / Liu, H. / Nix, J. / Xu, R. / Knoverek, C.R. / Bowman, G.R. / Amarasinghe, G.K. / Sibley, L.D.
History
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST


Theoretical massNumber of molelcules
Total (without water)73,3601
Polymers73,3601
Non-polymers00
Water00
1
A: Signal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST

A: Signal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST


Theoretical massNumber of molelcules
Total (without water)146,7202
Polymers146,7202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2130 Å2
ΔGint-21 kcal/mol
Surface area53930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.960, 163.920, 226.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Signal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST / Transcription factor ISGF-3 components p91/p84


Mass: 73359.930 Da / Num. of mol.: 1 / Fragment: STAT1-binding region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Toxoplasma gondii GT1 (eukaryote)
Gene: STAT1, TGRH88_087790 / Production host: Escherichia coli (E. coli) / References: UniProt: P42224, UniProt: A0A7J6KA90

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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: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.3-6.0, 3 M sodium chloride and 50 mM sodium citrate tribasic
PH range: 6.0-6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 18, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.97→46.64 Å / Num. obs: 23640 / % possible obs: 100 % / Redundancy: 29 % / Biso Wilson estimate: 79.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.033 / Rrim(I) all: 0.179 / Rsym value: 0.176 / Net I/σ(I): 20.3
Reflection shellResolution: 2.97→3.15 Å / Redundancy: 28.4 % / Rmerge(I) obs: 1.961 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3764 / CC1/2: 0.874 / Rpim(I) all: 0.372 / Rrim(I) all: 1.997 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BF5

1bf5


Resolution: 2.97→46.64 Å / SU ML: 0.3952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.8527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 1160 4.92 %
Rwork0.248 22425 -
obs0.25 23585 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.33 Å2
Refinement stepCycle: LAST / Resolution: 2.97→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 0 0 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014451
X-RAY DIFFRACTIONf_angle_d1.12796076
X-RAY DIFFRACTIONf_chiral_restr0.0602711
X-RAY DIFFRACTIONf_plane_restr0.0066788
X-RAY DIFFRACTIONf_dihedral_angle_d6.52262666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.110.48211380.37722755X-RAY DIFFRACTION99.9
3.11-3.270.37871570.32532735X-RAY DIFFRACTION99.9
3.27-3.470.33751240.26422808X-RAY DIFFRACTION99.9
3.47-3.740.34821420.24762755X-RAY DIFFRACTION99.83
3.74-4.120.28571350.22442798X-RAY DIFFRACTION99.97
4.12-4.710.23371490.21562791X-RAY DIFFRACTION99.97
4.71-5.940.26311560.2392836X-RAY DIFFRACTION99.93
5.94-46.640.26761590.24352947X-RAY DIFFRACTION99.84

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