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- PDB-3wwt: Crystal Structure of the Y3:STAT1ND complex -

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Basic information

Entry
Database: PDB / ID: 3wwt
TitleCrystal Structure of the Y3:STAT1ND complex
Components
  • C' protein
  • Signal transducer and activator of transcription 1-alpha/beta
KeywordsTRANSCRIPTION/VIRAL PROTEIN / alpha protein / interferon inhibition / signal transduction / transcriptional activation / TRANSCRIPTION-VIRAL PROTEIN complex
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-9-mediated signaling pathway / tumor necrosis factor receptor binding / Signaling by cytosolic FGFR1 fusion mutants / blood circulation / Interleukin-35 Signalling / Interleukin-27 signaling / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of mesenchymal cell proliferation / macrophage derived foam cell differentiation / histone acetyltransferase binding / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / response to type II interferon / ubiquitin-like protein ligase binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of endothelial cell proliferation / cell surface receptor signaling pathway via JAK-STAT / cellular response to organic cyclic compound / Regulation of IFNA/IFNB signaling / positive regulation of interferon-alpha production / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interferon-beta / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / response to mechanical stimulus / negative regulation of canonical NF-kappaB signal transduction / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / positive regulation of defense response to virus by host / response to cAMP / tumor necrosis factor-mediated signaling pathway / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Downstream signal transduction / negative regulation of angiogenesis / response to nutrient / transcription corepressor binding / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / protein phosphatase 2A binding / virion component / response to cytokine / promoter-specific chromatin binding / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / PKR-mediated signaling / response to hydrogen peroxide / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / ISG15 antiviral mechanism / response to peptide hormone / defense response / transcription coactivator binding / cellular response to type II interferon / cellular response to insulin stimulus / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon gamma signaling / Interferon alpha/beta signaling / 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 / host cell cytoplasm / DNA-binding transcription factor activity, RNA polymerase II-specific / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / response to xenobiotic stimulus / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / dendrite / chromatin / nucleolus / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Paramyxovirus non-structural protein C / Paramyxovirus non-structural protein C / 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 / : / Signal transducer and activator of transcription, linker domain ...Paramyxovirus non-structural protein C / Paramyxovirus non-structural protein C / 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 / : / Signal transducer and activator of transcription, linker 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 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 / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
C' protein / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Sendai virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOda, K. / Sakaguchi, T. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2015
Title: Structural Basis of the Inhibition of STAT1 Activity by Sendai Virus C Protein.
Authors: Oda, K. / Matoba, Y. / Irie, T. / Kawabata, R. / Fukushi, M. / Sugiyama, M. / Sakaguchi, T.
History
DepositionJun 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 2, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 18, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / audit_author / cell / database_2 / diffrn / entity / entity_name_com / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / pdbx_xplor_file / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen / symmetry
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _audit_author.name / _cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.address_1 / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_database_status.deposit_site / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_free_error / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_data_cutoff_high_absF / _refine.pdbx_data_cutoff_low_absF / _refine.pdbx_isotropic_thermal_model / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_rejects / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.pdbx_CASP_flag / _struct_ref_seq_dif.details / _symmetry.space_group_name_Hall
Description: Model orientation/position
Details: the model was re-refined by using phenix program to reduce the R factor and R free.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 12, 2022Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.deposit_site
Revision 2.2Nov 8, 2023Group: 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
B: C' protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7523
Polymers31,7122
Non-polymers401
Water2,936163
1
A: Signal transducer and activator of transcription 1-alpha/beta
B: C' protein
hetero molecules

A: Signal transducer and activator of transcription 1-alpha/beta
B: C' protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5046
Polymers63,4244
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area6490 Å2
ΔGint-37 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.270, 72.270, 197.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Components on special symmetry positions
IDModelComponents
11B-301-

CA

21B-1143-

HOH

31B-1155-

HOH

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Components

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


Mass: 17156.125 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Plasmid: pCold ProS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42224
#2: Protein C' protein


Mass: 14555.976 Da / Num. of mol.: 1 / Fragment: UNP residues 109-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sendai virus (Z) / Gene: P/V/C / Plasmid: pCold ProS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04862
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0.298 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG400, 0.2M CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2014
RadiationMonochromator: FIXED EXIST Si 111 DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 21786 / Num. obs: 21429 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.042 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.0711.70.43221000.414199.6
2.07-2.1511.70.31721110.428199.7
2.15-2.2511.60.22221140.477199.5
2.25-2.3711.70.16521090.509199.3
2.37-2.5211.60.12421190.581199.1
2.52-2.7111.70.09521160.686199
2.71-2.9911.90.07921500.912198.8
2.99-3.42120.07721581.629198.4
3.42-4.31120.06421802.425197.8
4.31-10012.40.05222722.088193.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660+SVNrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YVL

1yvl


Resolution: 2→34.02 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1091 5.09 %RANDOM
Rwork0.2049 20336 --
obs0.2066 21427 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.74 Å2
Refinement stepCycle: LAST / Resolution: 2→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 1 163 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722023
X-RAY DIFFRACTIONf_angle_d0.78392722
X-RAY DIFFRACTIONf_chiral_restr0.0413288
X-RAY DIFFRACTIONf_plane_restr0.0045349
X-RAY DIFFRACTIONf_dihedral_angle_d4.8078252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.28071430.23012471X-RAY DIFFRACTION99.13
2.09-2.20.28911440.22562499X-RAY DIFFRACTION99.85
2.2-2.340.25271230.22242519X-RAY DIFFRACTION99.55
2.34-2.520.23851260.21812516X-RAY DIFFRACTION99.36
2.52-2.770.24691230.22052536X-RAY DIFFRACTION99.14
2.77-3.170.25991490.21442536X-RAY DIFFRACTION98.97
3.17-40.23421630.19132558X-RAY DIFFRACTION98.48
4-34.020.20151200.19192701X-RAY DIFFRACTION95.4

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