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- PDB-1yvl: Structure of Unphosphorylated STAT1 -

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Basic information

Entry
Database: PDB / ID: 1yvl
TitleStructure of Unphosphorylated STAT1
Components
  • 5-residue peptide
  • Signal transducer and activator of transcription 1-alpha/beta
KeywordsSIGNALING PROTEIN
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
Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / 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, DNA-binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction ...Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / 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, DNA-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 / SH2 domain / SHC Adaptor Protein / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / p53-like transcription factor, DNA-binding / EF-hand / Recoverin; domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsMao, X. / Ren, Z. / Parker, G.N. / Sondermann, H. / Pastorello, M.A. / Wang, W. / McMurray, J.S. / Demeler, B. / Darnell Jr., J.E. / Chen, X.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural bases of unphosphorylated STAT1 association and receptor binding.
Authors: Mao, X. / Ren, Z. / Parker, G.N. / Sondermann, H. / Pastorello, M.A. / Wang, W. / McMurray, J.S. / Demeler, B. / Darnell, J.E. / Chen, X.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 1-alpha/beta
B: Signal transducer and activator of transcription 1-alpha/beta
C: 5-residue peptide
D: 5-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9646
Polymers161,5704
Non-polymers3942
Water00
1
A: Signal transducer and activator of transcription 1-alpha/beta
C: 5-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9823
Polymers80,7852
Non-polymers1971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area34390 Å2
MethodPISA
2
B: Signal transducer and activator of transcription 1-alpha/beta
D: 5-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9823
Polymers80,7852
Non-polymers1971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-11 kcal/mol
Surface area34120 Å2
MethodPISA
3
A: Signal transducer and activator of transcription 1-alpha/beta
C: 5-residue peptide
hetero molecules

A: Signal transducer and activator of transcription 1-alpha/beta
C: 5-residue peptide
hetero molecules

B: Signal transducer and activator of transcription 1-alpha/beta
D: 5-residue peptide
hetero molecules

B: Signal transducer and activator of transcription 1-alpha/beta
D: 5-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,92812
Polymers323,1408
Non-polymers7884
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area16090 Å2
ΔGint-73 kcal/mol
Surface area125330 Å2
MethodPISA
4
A: Signal transducer and activator of transcription 1-alpha/beta
C: 5-residue peptide
hetero molecules

B: Signal transducer and activator of transcription 1-alpha/beta
D: 5-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9646
Polymers161,5704
Non-polymers3942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area5730 Å2
ΔGint-30 kcal/mol
Surface area64980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.553, 102.553, 646.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 80044.258 Da / Num. of mol.: 2 / Fragment: residues 1-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Plasmid: pET20b(+) (Novagen) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-CodonPlus(DE3)-RP (Stratagene)
References: UniProt: P42224
#2: Protein/peptide 5-residue peptide


Mass: 740.697 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized, the sequence is derived from human interferon gamma receptor alpha chain
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
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: 3.1 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 25, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 92679
Reflection shellResolution: 3→3.11 Å / % possible all: 98.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 1542 RANDOM
Rwork0.24 --
all-76067 -
obs-65278 -
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10861 0 2 0 10863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4

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