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- PDB-1bf5: TYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bf5
TitleTYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX
Components
  • DNA (5'-D(*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*G P*C)-3')
  • DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*T P*G)-3')
  • SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA
KeywordsGENE REGULATION/DNA / COMPLEX (SH2 DOMAIN-DNA) / SH2 DOMAIN / TRANSCRIPTION FACTOR / GENE REGULATION-DNA 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 / positive regulation of mesenchymal cell proliferation / NOTCH3 Intracellular Domain Regulates Transcription / histone acetyltransferase binding / macrophage derived foam cell differentiation / Interleukin-20 family signaling / negative regulation of endothelial cell proliferation / Interleukin-6 signaling / type I interferon-mediated signaling pathway / response to type II interferon / ubiquitin-like protein ligase binding / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / cell surface receptor signaling pathway via JAK-STAT / cellular response to organic cyclic compound / Regulation of IFNA/IFNB signaling / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interferon-beta / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / response to mechanical stimulus / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / 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 / negative regulation of angiogenesis / Downstream signal transduction / response to nutrient / transcription corepressor binding / protein phosphatase 2A binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of erythrocyte differentiation / 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 / response to hydrogen peroxide / PKR-mediated signaling / defense response / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / transcription coactivator binding / response to peptide hormone / ISG15 antiviral mechanism / cellular response to type II interferon / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / 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 / defense response to virus / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding
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 domain / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction ...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 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 / 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
DNA / DNA (> 10) / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsKuriyan, J. / Zhao, Y. / Chen, X. / Vinkemeier, U. / Jeruzalmi, D. / Darnell Jr., J.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA.
Authors: Chen, X. / Vinkemeier, U. / Zhao, Y. / Jeruzalmi, D. / Darnell Jr., J.E. / Kuriyan, J.
History
DepositionMay 27, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 19, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Mar 7, 2018Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.5Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*G P*C)-3')
C: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*T P*G)-3')
A: SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA


Theoretical massNumber of molelcules
Total (without water)77,6883
Polymers77,6883
Non-polymers00
Water0
1
A: SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA

B: DNA (5'-D(*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*G P*C)-3')
C: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*T P*G)-3')
A: SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA


Theoretical massNumber of molelcules
Total (without water)144,3464
Polymers144,3464
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)76.600, 148.200, 181.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsA CRYSTALLOGRAPHIC 2-FOLD AXIS PASSES THROUGH THE CENTER OF THE DNA DUPLEX. THE ASYMMETRIC UNIT CONTAINS HALF OF THE DUPLEX, AND THUS THE OPERATION OF THE TWO-FOLD AXIS RESULTS IN A NET 1.0 OCCUPANCY WITHIN THE ASYMMETRIC UNIT.

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Components

#1: DNA chain DNA (5'-D(*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*G P*C)-3')


Mass: 5475.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: DNA chain DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*T P*G)-3')


Mass: 5555.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA / TRANSCRIPTION FACTOR ISGF-3 COMPONENTS P91/P84 / STAT-1


Mass: 66657.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 136-710 / Mutation: PHOSPHORYLATED TYR 701
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P42224

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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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA ACETATE11
3KCL11
4MGCL211
5NAN311
6PEG 40011
7WATER12
8PEG 40012
9NAN312
10MGCL212
11KCL12
12NA ACETATE12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.12 mMprotein1drop
2100 mMsodium acetate1reservoirpH5.0
3100 mM1reservoirKCl
420 mM1reservoirMgCl2
53 %PEG4001reservoir
60.01 %1reservoirNaN3
71
81
91
101
111
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: AREA DETECTOR / Date: Jan 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 23301 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.198
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Num. measured all: 261200
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 72.1 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2041 10 %RANDOM
Rwork0.227 ---
obs0.227 20526 89.8 %-
all-20526 --
Displacement parametersBiso mean: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-3.462 Å20 Å20 Å2
2--6.882 Å20 Å2
3----10.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 732 0 0 5117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2.289

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