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- PDB-1bg1: TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bg1
TitleTRANSCRIPTION FACTOR STAT3B/DNA COMPLEX
Components
  • DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
  • PROTEIN (TRANSCRIPTION FACTOR STAT3B)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / PROTEIN-DNA COMPLEX / CYTOKINE ACTIVATION / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


STAT3 nuclear events downstream of ALK signaling / MET activates STAT3 / Interleukin-37 signaling / Interleukin-10 signaling / PTK6 Activates STAT3 / Signaling by ALK / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling ...STAT3 nuclear events downstream of ALK signaling / MET activates STAT3 / Interleukin-37 signaling / Interleukin-10 signaling / PTK6 Activates STAT3 / Signaling by ALK / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / RNA sequestering activity / Interleukin-20 family signaling / Interleukin-23 signaling / Interleukin-27 signaling / Interleukin-6 signaling / radial glial cell differentiation / negative regulation of primary miRNA processing / Downstream signal transduction / Interleukin-35 Signalling / retinal rod cell differentiation / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / negative regulation of hydrogen peroxide biosynthetic process / T-helper 17 type immune response / negative regulation of neuron migration / PKR-mediated signaling / negative regulation of inflammatory response to wounding / primary miRNA binding / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / response to leptin / regulation of feeding behavior / sexual reproduction / interleukin-9-mediated signaling pathway / nuclear glucocorticoid receptor binding / interleukin-10-mediated signaling pathway / regulation of cellular response to hypoxia / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / interleukin-2-mediated signaling pathway / acetylation-dependent protein binding / cellular response to leptin stimulus / interleukin-15-mediated signaling pathway / interleukin-23-mediated signaling pathway / postsynapse to nucleus signaling pathway / negative regulation of stem cell differentiation / astrocyte differentiation / regulation of mitochondrial membrane permeability / positive regulation of cytokine production involved in inflammatory response / phosphorylation / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / eating behavior / temperature homeostasis / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / lncRNA binding / cellular response to cytokine stimulus / positive regulation of ATP biosynthetic process / positive regulation of interleukin-10 production / positive regulation of vascular endothelial growth factor production / somatic stem cell population maintenance / regulation of multicellular organism growth / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / energy homeostasis / positive regulation of phagocytosis / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / negative regulation of autophagy / transforming growth factor beta receptor signaling pathway / protein sequestering activity / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / response to ischemia / acute-phase response / positive regulation of interleukin-8 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA transcription by RNA polymerase II / modulation of chemical synaptic transmission / cytokine-mediated signaling pathway / chromatin DNA binding / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / negative regulation of inflammatory response / Schaffer collateral - CA1 synapse / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of angiogenesis / protein import into nucleus / positive regulation of tumor necrosis factor production / glucose homeostasis / response to estradiol / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / protein phosphatase binding / transcription regulator complex
Similarity search - Function
STAT3, SH2 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 ...STAT3, SH2 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
DNA / DNA (> 10) / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsBecker, S. / Groner, B. / Muller, C.W.
CitationJournal: Nature / Year: 1998
Title: Three-dimensional structure of the Stat3beta homodimer bound to DNA.
Authors: Becker, S. / Groner, B. / Muller, C.W.
History
DepositionJun 3, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 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_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(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: PROTEIN (TRANSCRIPTION FACTOR STAT3B)


Theoretical massNumber of molelcules
Total (without water)73,6572
Polymers73,6572
Non-polymers00
Water2,774154
1
B: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: PROTEIN (TRANSCRIPTION FACTOR STAT3B)

B: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: PROTEIN (TRANSCRIPTION FACTOR STAT3B)


Theoretical massNumber of molelcules
Total (without water)147,3134
Polymers147,3134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)174.000, 174.000, 79.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41

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Components

#1: DNA chain DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')


Mass: 5441.540 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 18-MER CHEMICALLY SYNTHESIZED, ACTIVE FORM IS 17-MER DUPLEX WITH OVERHANGING ENDS
#2: Protein PROTEIN (TRANSCRIPTION FACTOR STAT3B)


Mass: 68215.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42227
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: protein-DNA solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.074 mMprotein1drop
220 mMHEPES1drop
3200 mM1dropNaCl
410 mM1dropMgCl2
55 mMdithiothreitol1drop
60.5 mMPMSF1drop
80.1-0.4 M1reservoirNaCl
95 mM1reservoirMgSO4
7DNA duplex1drop
1050 mMMES1reservoir
110.1 Mammonium acetate1reservoir
1210 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.987
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 56005 / Num. obs: 56005 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 273455
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHARPphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.25→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2881 5 %RANDOM
Rwork0.246 ---
obs-55978 94.4 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 360 0 154 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.42.5
X-RAY DIFFRACTIONx_mcangle_it3.43
X-RAY DIFFRACTIONx_scbond_it3.83
X-RAY DIFFRACTIONx_scangle_it53.5
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45

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