4A3N

Crystal Structure of HMG-BOX of Human SOX17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Human Transcription Factor Sry-Related Box 17 Binding to DNA.

Gao, N.Jiang, W.Gao, H.Cheng, Z.Qian, H.Si, S.Xie, Y.

(2013) Protein Pept.Lett. 20: 481


  • PubMed Abstract: 
  • Sry-related box (Sox) transcription factors share a conserved high-mobility-group box domain (HMG-domain) that binds DNA in the minor groove and bends DNA for further assembly of transcriptional machineries. During organogenesis, each member of the S ...

    Sry-related box (Sox) transcription factors share a conserved high-mobility-group box domain (HMG-domain) that binds DNA in the minor groove and bends DNA for further assembly of transcriptional machineries. During organogenesis, each member of the Sox family triggers a specific cell lineage differentiation, indicating that their interactions with DNA are different from each other. Therefore, investigating structural rearrangement of each Sox transcription factor HMG-domain upon binding to DNA would help to elucidate the distinctive molecular mechanism by which they interact with DNA. Previous studies have determined the crystal structures of Sox2 HMG-domain/DNA, Sox4 HMGdomain/ DNA, Sox9 HMG-domain/DNA and Sox17 HMG-domain/DNA complexes. However, major gaps remain in the structural information on the Sox transcription factor HMG-domains. Here, we report the crystal structure of the human Sox17 HMG-domain alone at 2.4 A resolution. Comparing this structure and the structure of the mouse Sox17 HMGdomain/ DNA complex provides structural understanding of the mechanism of Sox17 binding to DNA. Specifically, after electrostatic interactions attract Sox17 to DNA, Asn73, Ser99, and Trp106 form hydrogen bonds with DNA, Arg70, Lys80, Arg83, His94, and Asn95 on Sox17 undergo conformational changes and form hydrogen bonds with DNA, contributing to the electrostatic interaction between Sox17 and DNA.


    Related Citations: 
    • The Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology But Selective Protein Interaction Platforms.
      Palasingam, P.,Jauch, R.,Ng, C.K.L.,Kolatkar, P.R.
      (2009) J.Mol.Biol. 388: 619


    Organizational Affiliation

    Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical college, Tian Tan Xi Li, Beijing 100050, People’s Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION FACTOR SOX-17
A
71Homo sapiensMutation(s): 0 
Gene Names: SOX17
Find proteins for Q9H6I2 (Homo sapiens)
Go to Gene View: SOX17
Go to UniProtKB:  Q9H6I2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.281α = 90.00
b = 22.525β = 129.09
c = 66.668γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2013-03-20
    Type: Data collection, Database references