[English] 日本語
Yorodumi
- PDB-4y5w: Transcription factor-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y5w
TitleTranscription factor-DNA complex
Components
  • DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
  • Signal transducer and activator of transcription 6
KeywordsTRANSCRIPTION/DNA / regulation / DNA binding / innate immune / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / interleukin-4-mediated signaling pathway / isotype switching to IgE isotypes / mammary gland epithelial cell proliferation ...regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / interleukin-4-mediated signaling pathway / isotype switching to IgE isotypes / mammary gland epithelial cell proliferation / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / Downstream signal transduction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coactivator binding / defense response / cytokine-mediated signaling pathway / response to peptide hormone / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / regulation of cell population proliferation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / 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 ...STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / 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. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Signal transducer and activator of transcription 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å
AuthorsLi, J. / Niu, F. / Ouyang, S. / Liu, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for DNA recognition by STAT6
Authors: Li, J. / Rodriguez, J.P. / Niu, F. / Pu, M. / Wang, J. / Hung, L.W. / Shao, Q. / Zhu, Y. / Ding, W. / Liu, Y. / Da, Y. / Yao, Z. / Yang, J. / Zhao, Y. / Wei, G.H. / Cheng, G. / Liu, Z.J. / Ouyang, S.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Data collection
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 16, 2016Group: Database references
Revision 1.4Nov 30, 2016Group: Database references
Revision 1.5Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal transducer and activator of transcription 6
B: Signal transducer and activator of transcription 6
D: Signal transducer and activator of transcription 6
E: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
M: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
N: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
C: Signal transducer and activator of transcription 6


Theoretical massNumber of molelcules
Total (without water)273,3148
Polymers273,3148
Non-polymers00
Water4,161231
1
A: Signal transducer and activator of transcription 6
M: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
N: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
C: Signal transducer and activator of transcription 6


Theoretical massNumber of molelcules
Total (without water)136,6574
Polymers136,6574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Signal transducer and activator of transcription 6
D: Signal transducer and activator of transcription 6
E: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)136,6574
Polymers136,6574
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.298, 94.241, 147.785
Angle α, β, γ (deg.)99.85, 101.73, 89.93
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Signal transducer and activator of transcription 6 / IL-4 Stat


Mass: 61577.602 Da / Num. of mol.: 4 / Fragment: UNP residues 113-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT6 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: P42226
#2: DNA chain DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')


Mass: 6824.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Mass: 6677.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 62.65 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate (pH 5.6), 0.1M NaCl, 20% isopropyl alcohol and 8% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 57478 / % possible obs: 98 % / Redundancy: 3.5 % / Rsym value: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.65 / Rsym value: 0.4 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHENIXmodel building
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5U

4y5u


Resolution: 3.104→38.807 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 2918 5.08 %
Rwork0.2496 --
obs0.2511 57478 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.104→38.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15038 1804 0 231 17073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817347
X-RAY DIFFRACTIONf_angle_d1.06423773
X-RAY DIFFRACTIONf_dihedral_angle_d19.3836666
X-RAY DIFFRACTIONf_chiral_restr0.0452683
X-RAY DIFFRACTIONf_plane_restr0.0062733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1038-3.15460.3618840.34511473X-RAY DIFFRACTION51
3.1546-3.2090.3594940.32531750X-RAY DIFFRACTION61
3.209-3.26730.3393810.31811997X-RAY DIFFRACTION67
3.2673-3.33010.37011040.31582095X-RAY DIFFRACTION72
3.3301-3.39810.32441210.30542239X-RAY DIFFRACTION77
3.3981-3.47190.36021330.29172442X-RAY DIFFRACTION85
3.4719-3.55260.30531310.27732646X-RAY DIFFRACTION91
3.5526-3.64140.29061510.27032860X-RAY DIFFRACTION97
3.6414-3.73980.32581740.26692783X-RAY DIFFRACTION98
3.7398-3.84970.27391570.26162821X-RAY DIFFRACTION98
3.8497-3.97390.25931480.24962903X-RAY DIFFRACTION98
3.9739-4.11580.2841400.24422838X-RAY DIFFRACTION98
4.1158-4.28030.30061700.23182879X-RAY DIFFRACTION98
4.2803-4.47490.22281450.23782858X-RAY DIFFRACTION98
4.4749-4.71040.22481410.21542840X-RAY DIFFRACTION98
4.7104-5.0050.26041460.22892873X-RAY DIFFRACTION99
5.005-5.39050.27811360.24532866X-RAY DIFFRACTION99
5.3905-5.93120.27421630.25712874X-RAY DIFFRACTION99
5.9312-6.78550.28931810.26882847X-RAY DIFFRACTION99
6.7855-8.5340.26921800.24232839X-RAY DIFFRACTION99
8.534-38.80960.23171380.20242837X-RAY DIFFRACTION98

+
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