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- PDB-7nuf: Vaccinia virus protein 018 in complex with STAT1 -

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Basic information

Entry
Database: PDB / ID: 7nuf
TitleVaccinia virus protein 018 in complex with STAT1
Components
  • Signal transducer and activator of transcription 1-alpha/beta
  • Uncharacterized protein 18
KeywordsTRANSCRIPTION / Transcription factor / Inhibitor / Complex / Viral
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 / blood circulation / positive regulation of mesenchymal cell proliferation / NOTCH3 Intracellular Domain Regulates Transcription / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / histone acetyltransferase binding / : / negative regulation of endothelial cell proliferation / positive regulation of interferon-alpha production / ubiquitin-like protein ligase binding / Regulation of IFNA/IFNB signaling / : / response to type II interferon / RNA polymerase II core promoter sequence-specific DNA binding / cell surface receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / cellular response to interferon-beta / Regulation of IFNG signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Growth hormone receptor signaling / negative regulation of canonical NF-kappaB signal transduction / response to mechanical stimulus / Signaling by CSF3 (G-CSF) / positive regulation of defense response to virus by host / response to cAMP / tumor necrosis factor-mediated signaling pathway / Downstream signal transduction / response to nutrient / response to cytokine / negative regulation of angiogenesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / positive regulation of smooth muscle cell proliferation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signaling by SCF-KIT / Inactivation of CSF3 (G-CSF) signaling / PKR-mediated signaling / response to hydrogen peroxide / transcription coactivator binding / defense response / cellular response to type II interferon / ISG15 antiviral mechanism / response to peptide hormone / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RUNX2 expression and activity / Interferon gamma signaling / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / histone binding / double-stranded DNA binding / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / response to xenobiotic stimulus / axon / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / dendrite / regulation of transcription by RNA polymerase II / chromatin / nucleolus / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / 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 / identical protein binding
Similarity search - Function
Orthopoxvirus C10L / Orthopoxvirus C10L protein / 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 ...Orthopoxvirus C10L / Orthopoxvirus C10L protein / 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 / p53-like transcription factor, DNA-binding / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / OPG024 protein / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Vaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00040159011 Å
AuthorsPantelejevs, T. / Talbot-Cooper, C. / Smith, G.L. / Hyvonen, M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Wellcome Trust United Kingdom
Citation
Journal: Cell Host Microbe / Year: 2022
Title: Poxviruses and paramyxoviruses use a conserved mechanism of STAT1 antagonism to inhibit interferon signaling.
Authors: Talbot-Cooper, C. / Pantelejevs, T. / Shannon, J.P. / Cherry, C.R. / Au, M.T. / Hyvonen, M. / Hickman, H.D. / Smith, G.L.
#1: Journal: Biorxiv / Year: 2021
Title: A strategy to suppress STAT1 signalling conserved in pathogenic poxviruses and paramyxoviruses
Authors: Talbot-Cooper, C. / Pantelejevs, T. / Shannon, J.P. / Cherry, C.R. / Au, M.T. / Hyvonen, M. / Hickman, H.D. / Smith, G.L.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 25, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Uncharacterized protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7904
Polymers65,6502
Non-polymers1402
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-22 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.056, 37.468, 115.476
Angle α, β, γ (deg.)90.000, 116.193, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 63306.715 Da / Num. of mol.: 1 / Mutation: Delta183-190, H182A, E393A, E394A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P42224
#2: Protein/peptide Uncharacterized protein 18


Mass: 2343.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus (strain Western Reserve) / References: UniProt: P17356
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 300:300 nl drop of protein:condition Protein: 10 mg/ml STAT1:peptide complex in 20 mM Tris pH8.0, 300 mM NaCl, 1 mM EDTA, 5 mM TCEP Condition: 16% PEG 3350 (w/v), 175 mM KCl, 125 mM NH4SO4,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→80.42 Å / Num. obs: 44523 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.4700956008 Å2 / CC1/2: 1 / Rrim(I) all: 0.124 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.04 Å / Redundancy: 4.3 % / Num. unique obs: 2186 / CC1/2: 0.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YVL

1yvl


Resolution: 2.00040159011→55.7514233699 Å / SU ML: 0.356742212896 / Cross valid method: FREE R-VALUE / σ(F): 1.3281749626 / Phase error: 33.2966966352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256435758256 2129 4.90462587541 %
Rwork0.223694724312 41279 -
obs0.225254064685 43408 97.2205424534 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.7300126627 Å2
Refinement stepCycle: LAST / Resolution: 2.00040159011→55.7514233699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 8 200 4657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088533905174550
X-RAY DIFFRACTIONf_angle_d1.309220612826144
X-RAY DIFFRACTIONf_chiral_restr0.0946982534527683
X-RAY DIFFRACTIONf_plane_restr0.00685488302762776
X-RAY DIFFRACTIONf_dihedral_angle_d16.34887835522770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00040159011-2.04690.4358278839731010.4118833500752061X-RAY DIFFRACTION73.7632207438
2.0469-2.09810.437728198641470.3870478671282562X-RAY DIFFRACTION91.7061611374
2.0981-2.15490.4107469926811470.3552525861872740X-RAY DIFFRACTION98.599726776
2.1549-2.21830.3370504277011520.343836253512807X-RAY DIFFRACTION99.5625841184
2.2183-2.28990.3981915353341540.3251309176742748X-RAY DIFFRACTION99.5881949211
2.2899-2.37170.3960939098881370.3032423465342798X-RAY DIFFRACTION99.3231810491
2.3717-2.46670.3238964157611500.2908126726732795X-RAY DIFFRACTION99.2250673854
2.4667-2.57890.3152150639191580.2659009174232751X-RAY DIFFRACTION99.487004104
2.5789-2.71490.2812463136721330.2537852400382853X-RAY DIFFRACTION99.4007989348
2.7149-2.8850.2455655254631460.2455900993962843X-RAY DIFFRACTION99.7330663997
2.885-3.10770.2803187523691390.2362972048262803X-RAY DIFFRACTION99.5937711578
3.1077-3.42040.2631411381961440.2187344936682827X-RAY DIFFRACTION99.4976557267
3.4204-3.91530.212112066381300.2000731111572846X-RAY DIFFRACTION99.5317725753
3.9153-4.93240.1951556840711540.1694165279362836X-RAY DIFFRACTION99.4346524776
4.9324-55.75142336990.2145417891011370.1869255029173009X-RAY DIFFRACTION99.4310998736
Refinement TLS params.Method: refined / Origin x: -89.1890419879 Å / Origin y: -57.8580200028 Å / Origin z: 228.078960228 Å
111213212223313233
T0.358761647785 Å20.019380561577 Å2-0.0207558949665 Å2-0.256959105886 Å2-0.0153903645258 Å2--0.320084446234 Å2
L1.55791342616 °20.534789681227 °2-1.37868689953 °2-0.712969012387 °2-0.959410755489 °2--2.30427894654 °2
S-0.0357539723573 Å °0.121179350201 Å °0.0282837425221 Å °-0.116705533226 Å °-0.0418816049528 Å °-0.0719928271705 Å °0.0644845736024 Å °0.0983666688642 Å °0.0672808148705 Å °
Refinement TLS groupSelection details: all

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