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

• 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)

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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

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.

Biological Assembly 1  

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

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

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-9	A	106	Homo sapiens	Mutation(s): 0  Gene Names: SGT82680, SOX9
UniProt & NIH Common Fund Data Resources
Find proteins for P48436 (Homo sapiens) Explore P48436  Go to UniProtKB:  P48436
PHAROS:  P48436 GTEx:  ENSG00000125398

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*CP*TP*TP*TP*GP*AP*GP*AP*AP*G)-3')	B	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*CP*TP*CP*AP*AP*AP*GP*AP*G)-3')	C	12	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.278 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 
• Space Group: C 2 2 2
• Diffraction Data: https://doi.org/10.18430/M34EUW

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.772	α = 90
b = 134.654	β = 90
c = 49.987	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
PHENIX	refinement
MolProbity	model building
XDS	data reduction

Structure Validation

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  

• 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