[English] 日本語
Yorodumi
- PDB-3cwg: Unphosphorylated mouse STAT3 core fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cwg
TitleUnphosphorylated mouse STAT3 core fragment
ComponentsSignal transducer and activator of transcription 3
KeywordsTRANSCRIPTION / STAT3 / Activator / Acute phase / Alternative splicing / Cytoplasm / DNA-binding / Nucleus / Phosphoprotein / SH2 domain / Transcription regulation
Function / homology
Function and homology information


STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling ...STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / Interleukin-20 family signaling / Interleukin-27 signaling / Interleukin-23 signaling / retinal rod cell differentiation / Interleukin-6 signaling / radial glial cell differentiation / Interleukin-35 Signalling / Downstream signal transduction / negative regulation of primary miRNA processing / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / negative regulation of neuron migration / PKR-mediated signaling / T-helper 17 type immune response / negative regulation of hydrogen peroxide biosynthetic process / negative regulation of inflammatory response to wounding / primary miRNA binding / response to leptin / sexual reproduction / interleukin-11-mediated signaling pathway / regulation of feeding behavior / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / cellular response to interleukin-17 / interleukin-9-mediated signaling pathway / regulation of cellular response to hypoxia / interleukin-2-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / nuclear glucocorticoid receptor binding / negative regulation of stem cell differentiation / acetylation-dependent protein binding / interleukin-15-mediated signaling pathway / cellular response to leptin stimulus / astrocyte differentiation / postsynapse to nucleus signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of glycolytic process / regulation of mitochondrial membrane permeability / positive regulation of vascular endothelial cell proliferation / temperature homeostasis / eating behavior / positive regulation of ATP biosynthetic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / cellular response to cytokine stimulus / somatic stem cell population maintenance / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / cellular response to organic cyclic compound / regulation of multicellular organism growth / positive regulation of vascular endothelial growth factor production / growth hormone receptor signaling pathway via JAK-STAT / energy homeostasis / signaling adaptor activity / negative regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / response to cytokine / acute-phase response / positive regulation of interleukin-8 production / response to ischemia / Schaffer collateral - CA1 synapse / mRNA transcription by RNA polymerase II / modulation of chemical synaptic transmission / chromatin DNA binding / response to peptide hormone / defense response / cytokine-mediated signaling pathway / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / protein import into nucleus / positive regulation of angiogenesis / nuclear receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / response to estradiol / glucose homeostasis / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding
Similarity search - Function
STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 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 transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 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
Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsRen, Z. / Mao, X. / Mertens, C. / Krishnaraj, R. / Qin, J. / Mandal, P.K. / Romanowshi, M.J. / McMurray, J.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of unphosphorylated STAT3 core fragment.
Authors: Ren, Z. / Mao, X. / Mertens, C. / Krishnaraj, R. / Qin, J. / Mandal, P.K. / Romanowski, M.J. / McMurray, J.S. / Chen, X.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal transducer and activator of transcription 3
B: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)128,8362
Polymers128,8362
Non-polymers00
Water00
1
A: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)64,4181
Polymers64,4181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)64,4181
Polymers64,4181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)254.779, 254.779, 123.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 64417.965 Da / Num. of mol.: 2 / Fragment: STAT3 Core Fragment, UNP residues (127-688)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stat3, Aprf / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P42227

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M Bis-tris, 0.5M ammonium sulfate, 12% PEG3350, 0.1mM KCl, 0.05M NaI, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115891 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2006 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115891 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 90262 / Num. obs: 84197 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.1
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6321 / % possible all: 70.6

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG1

1bg1


Resolution: 3.05→30 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The Matthews coefficient and the solvent content are unusual but it is correct. This is due to huge solvent channel in crystal packing.
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 7413 -RANDOM
Rwork0.2496 ---
all-87800 --
obs-80114 91.2 %-
Displacement parametersBiso mean: 97.14 Å2
Baniso -1Baniso -2Baniso -3
1-15.36 Å20 Å20 Å2
2--15.36 Å20 Å2
3----30.72 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8215 0 0 0 8215
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010651
X-RAY DIFFRACTIONx_angle_deg1.47677

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more