1GT0

Crystal structure of a POU/HMG/DNA ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of a POU/Hmg/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers

Remenyi, A., Lins, K., Nissen, L.J., Reinbold, R., Scholer, H.R., Wilmanns, M.

(2003) Genes Dev 17: 2048

  • DOI: 10.1101/gad.269303
  • Primary Citation of Related Structures:  
    1GT0

  • PubMed Abstract: 

    • Members of the POU and SOX transcription factor families exemplify the partnerships established between various transcriptional regulators during early embryonic development. Although functional cooperativity between key regulator proteins is pivotal for milestone decisions in mammalian development, little is known about the underlying molecular mechanisms ...

    Members of the POU and SOX transcription factor families exemplify the partnerships established between various transcriptional regulators during early embryonic development. Although functional cooperativity between key regulator proteins is pivotal for milestone decisions in mammalian development, little is known about the underlying molecular mechanisms. In this study, we focus on two transcription factors, Oct4 and Sox2, as their combination on DNA is considered to direct the establishment of the first three lineages in the mammalian embryo. Using experimental high-resolution structure determination, followed by model building and experimental validation, we found that Oct4 and Sox2 were able to dimerize onto DNA in distinct conformational arrangements. We demonstrate that the DNA enhancer region of their target genes is responsible for the correct spatial alignment of glue-like interaction domains on their surface. Interestingly, these surfaces frequently have redundant functions and are instrumental in recruiting various interacting protein partners.

    Organizational Affiliation: 

    Gene Expression Program, EMBL, 69117 Heidelberg, Germany. remenyi@itsa.ucsf.edu



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
OCTAMER-BINDING TRANSCRIPTION FACTOR 1C159Homo sapiensMutation(s): 2 
Gene Names: POU2F1, OCT1, OTF1
UniProt & NIH Common Fund Data Resources
Find proteins for P14859 (Homo sapiens)
Explore P14859 
Go to UniProtKB:  P14859
PHAROS:  P14859
GTEx:  ENSG00000143190
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION FACTOR SOX-2D80Mus musculusMutation(s): 0 
Gene Names: Sox2, Sox-2
UniProt & NIH Common Fund Data Resources
Find proteins for P48432 (Mus musculus)
Explore P48432 
Go to UniProtKB:  P48432
IMPC:  MGI:98364
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*CP*TP*TP*TP*GP*TP*TP*TP* GP*GP*AP* TP*GP*CP*TP*AP*AP*TP*GP*GP*GP*A)-3'A24Mus musculus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*TP*CP*CP*CP*AP*TP*TP*AP*GP* CP*AP*TP*CP*CP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'B24Mus musculus
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.8α = 90
b = 72.8β = 90
c = 172.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-30
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description
  • Version 1.2: 2019-07-24
    Changes: Data collection