[English] 日本語
Yorodumi
- PDB-8d3f: Crystal structure of human STAT1 in complex with the repeat regio... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of interferon-alpha production / Regulation of IFNA/IFNB signaling / response to type II interferon / cell surface receptor signaling pathway via JAK-STAT / response to mechanical stimulus / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Growth hormone receptor signaling / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interferon-beta / response to cAMP / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by CSF3 (G-CSF) / tumor necrosis factor-mediated signaling pathway / positive regulation of defense response to virus by host / response to cytokine / negative regulation of canonical NF-kappaB signal transduction / response to nutrient / Downstream signal transduction / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / transcription corepressor binding / positive regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / promoter-specific chromatin binding / response to hydrogen peroxide / defense response / Signaling by SCF-KIT / transcription coactivator binding / Inactivation of CSF3 (G-CSF) signaling / PKR-mediated signaling / response to peptide hormone / cellular response to type II interferon / ISG15 antiviral mechanism / 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 / defense response to virus / histone binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more