[English] 日本語
Yorodumi
- PDB-4e68: Unphosphorylated STAT3B core protein binding to dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4.0E+68
TitleUnphosphorylated STAT3B core protein binding to dsDNA
Components
  • DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
  • Signal transducer and activator of transcription 3
KeywordsTRANSCRIPTION/DNA / SH2 Domain / Protein DNA Complex / Signal Transducer / Activator of Transcription / Duplex DNA / Nucleus / Cytosol / 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 / negative regulation of 3'-UTR-mediated mRNA stabilization / Interleukin-20 family signaling / Interleukin-23 signaling / Interleukin-27 signaling / eye photoreceptor cell differentiation / radial glial cell differentiation / Interleukin-6 signaling / negative regulation of primary miRNA processing / Downstream signal transduction / Interleukin-35 Signalling / 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 / regulation of feeding behavior / positive regulation of extracellular matrix disassembly / primary miRNA binding / interleukin-11-mediated signaling pathway / negative regulation of inflammatory response to wounding / CCR5 chemokine receptor binding / cellular response to interleukin-17 / response to leptin / T-helper 17 cell lineage commitment / interleukin-9-mediated signaling pathway / inflammatory response to wounding / interleukin-10-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / nuclear glucocorticoid receptor binding / regulation of cellular response to hypoxia / acetylation-dependent protein binding / interleukin-15-mediated signaling pathway / interleukin-23-mediated signaling pathway / cellular response to leptin stimulus / negative regulation of stem cell differentiation / astrocyte differentiation / postsynapse to nucleus signaling pathway / signal transduction involved in regulation of gene expression / cell surface receptor signaling pathway via STAT / regulation of mitochondrial membrane permeability / positive regulation of cytokine production involved in inflammatory response / positive regulation of vascular endothelial cell proliferation / negative regulation of glycolytic process / growth hormone receptor signaling pathway / interleukin-6-mediated signaling pathway / interleukin-2-mediated signaling pathway / stem cell population maintenance / positive regulation of Notch signaling pathway / eating behavior / lncRNA binding / temperature homeostasis / cellular response to cytokine stimulus / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of ATP biosynthetic process / positive regulation of interleukin-10 production / 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 / cellular response to hormone stimulus / intracellular receptor signaling pathway / energy homeostasis / endoplasmic reticulum unfolded protein response / canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / response to cytokine / signaling adaptor activity / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / positive regulation of phagocytosis / response to ischemia / acute-phase response / negative regulation of autophagy / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / negative regulation of canonical NF-kappaB signal transduction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein sequestering activity / defense response / chromatin DNA binding / mRNA transcription by RNA polymerase II / positive regulation of miRNA transcription / positive regulation of interleukin-6 production / response to peptide hormone / modulation of chemical synaptic transmission / nuclear receptor activity / negative regulation of inflammatory response
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)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsCollie, G.W. / Parkinson, G.N. / Shah, R.
CitationJournal: Febs Lett. / Year: 2013
Title: Observation of unphosphorylated STAT3 core protein binding to target dsDNA by PEMSA and X-ray crystallography.
Authors: Nkansah, E. / Shah, R. / Collie, G.W. / Parkinson, G.N. / Palmer, J. / Rahman, K.M. / Bui, T.T. / Drake, A.F. / Husby, J. / Neidle, S. / Zinzalla, G. / Thurston, D.E. / Wilderspin, A.F.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)73,5772
Polymers73,5772
Non-polymers00
Water2,504139
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: Signal transducer and activator of transcription 3

B: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)147,1534
Polymers147,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area6670 Å2
ΔGint-61 kcal/mol
Surface area59930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.140, 174.140, 79.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
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: chemically synthesised DNA sequence / Source: (synth.) Synthetic (others)
#2: Protein Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 68135.125 Da / Num. of mol.: 1 / Fragment: STAT3 Core Fragment, residues (127-722)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aprf, Stat3, STAT3B / Plasmid: pET-32a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P42227
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO ISOFORM STAT3B

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.005M MgSO4, 0.1M ammonium acetate, 10% glycerol, 0.05M MES pH 5.6, 0.25M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.58→72.16 Å / Num. all: 36458 / Num. obs: 36458 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 75.03 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.2
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2721 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG1

1bg1


Resolution: 2.585→14.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.223 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 1810 5 %RANDOM
Rwork0.22532 ---
obs0.22778 34413 97.08 %-
all-34413 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.585→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 360 0 139 4998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194987
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9116810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2035556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.65224.928209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6731525
X-RAY DIFFRACTIONr_chiral_restr0.1260.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213569
LS refinement shellResolution: 2.585→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 137 -
Rwork0.361 2420 -
obs-2420 99.22 %

+
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