[English] 日本語
Yorodumi
- PDB-4zia: Crystal Structure of STAT3 N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zia
TitleCrystal Structure of STAT3 N-terminal domain
ComponentsSignal transducer and activator of transcription 3
KeywordsTRANSCRIPTION / STAT N-terminal domain
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 / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 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 / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / Interleukin-20 family signaling / Interleukin-23 signaling / Interleukin-27 signaling / Interleukin-6 signaling / radial glial cell differentiation / retinal rod cell differentiation / Downstream signal transduction / Interleukin-35 Signalling / negative regulation of primary miRNA processing / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / T-helper 17 type immune response / negative regulation of neuron migration / PKR-mediated signaling / response to leptin / negative regulation of inflammatory response to wounding / interleukin-10-mediated signaling pathway / primary miRNA binding / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / sexual reproduction / regulation of feeding behavior / interleukin-9-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-23-mediated signaling pathway / acetylation-dependent protein binding / cellular response to leptin stimulus / interleukin-15-mediated signaling pathway / astrocyte differentiation / negative regulation of stem cell differentiation / positive regulation of cytokine production involved in inflammatory response / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / phosphorylation / temperature homeostasis / eating behavior / interleukin-6-mediated signaling pathway / lncRNA binding / positive regulation of Notch signaling pathway / cellular response to cytokine stimulus / : / positive regulation of interleukin-10 production / somatic stem cell population maintenance / growth hormone receptor signaling pathway via JAK-STAT / positive regulation of vascular endothelial growth factor production / regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / energy homeostasis / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / negative regulation of cytokine production involved in inflammatory response / transforming growth factor beta receptor signaling pathway / negative regulation of autophagy / protein sequestering activity / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / acute-phase response / positive regulation of interleukin-8 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA transcription by RNA polymerase II / cytokine-mediated signaling pathway / chromatin DNA binding / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / protein import into nucleus / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / glucose homeostasis / response to estradiol / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / gene expression / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / transcription cis-regulatory region binding / regulation of cell cycle / protein dimerization activity / positive regulation of cell migration / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT3, SH2 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 ...Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT3, SH2 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 / 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
FORMIC ACID / NICKEL (II) ION / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHu, T. / Chopra, R.
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity.
Authors: Hu, T. / Yeh, J.E. / Pinello, L. / Jacob, J. / Chakravarthy, S. / Yuan, G.C. / Chopra, R. / Frank, D.A.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
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
C: Signal transducer and activator of transcription 3
D: Signal transducer and activator of transcription 3
E: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2048
Polymers76,0755
Non-polymers1293
Water1,13563
1
A: Signal transducer and activator of transcription 3
B: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4893
Polymers30,4302
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-9 kcal/mol
Surface area13240 Å2
MethodPISA
2
C: Signal transducer and activator of transcription 3
D: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4763
Polymers30,4302
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area12680 Å2
MethodPISA
3
E: Signal transducer and activator of transcription 3
hetero molecules

E: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4794
Polymers30,4302
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+7/41
Buried area2050 Å2
ΔGint-6 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.012, 109.012, 154.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-201-

NI

21E-201-

MG

31B-310-

HOH

41C-204-

HOH

-
Components

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


Mass: 15215.049 Da / Num. of mol.: 5 / Fragment: N-terminal domain (UNP residues 3-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stat3, Aprf / Plasmid: pNAT40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42227
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% v/v PEG 3350, 0.2M magnesium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 26131 / % possible obs: 99.6 % / Redundancy: 8 % / Rsym value: 0.075 / Net I/σ(I): 19.4
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1BGF

1bgf


Resolution: 2.7→20 Å / FOM work R set: 0.8022 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2701 1329 5.1 %
Rwork0.2362 24802 -
obs-26131 100 %
Solvent computationBsol: 46.352 Å2
Displacement parametersBiso max: 113.94 Å2 / Biso mean: 59.0826 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å20 Å2
2---5.27 Å20 Å2
3---10.54 Å2
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 5 63 5149
Biso mean--48.74 41.99 -
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.081
X-RAY DIFFRACTIONc_mcbond_it1.4081.5
X-RAY DIFFRACTIONc_scbond_it2.0752
X-RAY DIFFRACTIONc_mcangle_it2.4342
X-RAY DIFFRACTIONc_scangle_it3.3272.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.740.3816560.3598913969
2.74-2.770.3716540.3376933987
2.77-2.810.4425550.3317932987
2.81-2.850.467490.3175931980
2.85-2.90.3263400.3028946986
2.9-2.950.3513590.30159461005
2.95-30.3061460.3039929975
3-3.050.2896430.2818939982
3.05-3.110.399520.2812940992
3.11-3.170.3213450.3034944989
3.17-3.240.3358390.2643944983
3.24-3.320.2441650.23989571022
3.32-3.40.2596620.2493913975
3.4-3.490.2808520.259501002
3.49-3.590.2607520.22769541006
3.59-3.710.2642520.22219551007
3.71-3.840.2618500.2032932982
3.84-3.990.2383650.21549441009
3.99-4.170.2176520.20349591011
4.17-4.390.2075510.19259681019
4.39-4.660.2408450.19389611006
4.66-5.020.2458610.20579611022
5.02-5.510.2719450.24829811026
5.51-6.290.2866390.279510001039
6.29-7.840.325520.232710181070
7.84-200.2018480.186810521100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5fmt.paramfmt.top

+
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://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