GV

GeezerVison

The World Wide Web, restored to 800 pixels of glory.

Home|About|Gaming cabinet|Archives|How it works|Starter sites

On this site

  • Search
  • Advanced Search
  • Sequence Similarity Search
  • 3D Similarity Search
  • Chemical Similarity
  • Browse Annotations
  • New Entries
  • Unreleased Entries
  • PDB Statistics
  • Tools at-a-glance
  • Mol* (MolStar)
  • Sequence Annotations Viewer
  • Sequence Annotations in 3D
  • Genome View

This view

  • Original page
  • New address

GeezerVison is showing www.rcsb.org — RCSB PDB - 4EUW: Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution

  • Structure Summary
  • Structure
  • Annotations
  • Experiment
  • Sequence
  • Genome
  • Versions

  • FASTA Sequence
  • mmCIF Format
  • mmCIF Format (Header)
  • Legacy PDB Format
  • Legacy PDB Format (Header)
  • FASTA Sequence
  • PDBx/mmCIF Format
  • PDBx/mmCIF Format (gz)
  • BinaryCIF Format (gz)
  • Legacy PDB Format
  • Legacy PDB Format (gz)
  • PDBML/XML Format (gz)
  • Structure Factors (CIF)
  • Structure Factors (CIF - gz)
  • Validation Full (PDF - gz)
  • Validation (XML - gz)
  • Validation (CIF - gz)
  • Validation 2fo-fc coefficients (CIF - gz)
  • Validation fo-fc coefficients (CIF - gz)
  • Biological Assembly 1 (CIF - gz) 
  • Biological Assembly 1 (PDB - gz)
 Data API 

 4EUW | pdb_00004euw

Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution

  • PDB DOI: https://doi.org/10.2210/pdb4EUW/pdb
  • NAKB: 4EUW
  • Classification: TRANSCRIPTION/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2012-04-25 Released: 2012-06-13 
  • Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4EUW

This is version 1.4 of the entry. See complete history. 

Literature

  • Download Mendeley

Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology

To be published.
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

  • Total Structure Weight: 20.24 kDa 
  • Atom Count: 1,079 
  • Modeled Residue Count: 96 
  • Deposited Residue Count: 130 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:
  • 100%
  • 95%
  • 90%
  • 80%
  • 70%
  • 60%
  • 50%
  • 40%
  • 30%
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription factor SOX-9
A
106Homo sapiensMutation(s): 0 
Gene Names: SGT82680, SOX9
UniProt & NIH Common Fund Data Resources
Find proteins for P48436 (Homo sapiens)
Explore P48436 
Go to UniProtKB:  P48436
GTEx:  ENSG00000125398 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48436
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')
B
12Homo sapiens
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')
C
12Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.278 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Diffraction Data: 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.772α = 90
b = 134.654β = 90
c = 49.987γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
MolProbitymodel building
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2012-06-13 
    • Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Structure summary
  • Version 1.2: 2017-11-15
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description
You are visitor 01402503 — GeezerVison does not store the pages you look up.
Best viewed with Netscape Navigator 4.7 or Internet Explorer 6 at 800×600. No cookies required.