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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SOX-9106Homo sapiensMutation(s): 0 
Gene Names: SGT82680SOX9
UniProt & NIH Common Fund Data Resources
Find proteins for P48436 (Homo sapiens)
Explore P48436 
Go to UniProtKB:  P48436
PHAROS:  P48436
GTEx:  ENSG00000125398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48436
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')12Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')12Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

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Entry History 

Deposition Data

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