5KRB

GCNF DNA Binding Domain - Oct4 DR0 Complex

  • Classification: transcription/dna
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli BL21
  • Mutation(s): 

  • Deposited: 2016-07-07 Released: 2016-11-09 
  • Deposition Author(s): Weikum, E.R., Ortlund, E.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).

Weikum, E.R.Tuntland, M.L.Murphy, M.N.Ortlund, E.A.

(2016) J. Mol. Biol. 428: 4981-4992

  • DOI: 10.1016/j.jmb.2016.10.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oct4 is a transcription factor required for maintaining pluripotency and self-renewal in stem cells. Prior to differentiation, Oct4 must be silenced to allow for the development of the three germ layers in the developing embryo. This fine-tuning is c ...

    Oct4 is a transcription factor required for maintaining pluripotency and self-renewal in stem cells. Prior to differentiation, Oct4 must be silenced to allow for the development of the three germ layers in the developing embryo. This fine-tuning is controlled by the nuclear receptors (NRs), liver receptor homolog-1 (LRH-1) and germ cell nuclear factor (GCNF). Liver receptor homolog-1 is responsible for driving the expression of Oct4 where GCNF represses its expression upon differentiation. Both receptors bind to a DR0 motif located within the Oct4 promoter. Here, we present the first structure of mouse GCNF DNA-binding domain in complex with the Oct4 DR0. The overall structure revealed two molecules bound in a head-to-tail fashion on opposite sides of the DNA. Additionally, we solved the structure of the human LRH-1 DNA-binding domain bound to the same element. We explore the structural elements that govern Oct4 recognition by these two NRs.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 6 group A member 1
B, G
84Mus musculusMutation(s): 1 
Gene Names: Nr6a1 (Gcnf)
Find proteins for Q64249 (Mus musculus)
Go to UniProtKB:  Q64249
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3')A16Mus musculus
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')E16Mus musculus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.649α = 90.00
b = 69.469β = 90.00
c = 84.536γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited States1R01DK095750-01
National Institutes of Health/National Institute of General Medical SciencesUnited States1F31GM113397-01A1

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references
  • Version 1.2: 2017-04-05
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence