5KRB image
Deposition Date 2016-07-07
Release Date 2016-11-09
Last Version Date 2024-04-03
Entry Detail
PDB ID:
5KRB
Title:
GCNF DNA Binding Domain - Oct4 DR0 Complex
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3')
Chain IDs:A
Chain Length:16
Number of Molecules:1
Biological Source:Mus musculus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear receptor subfamily 6 group A member 1
Gene (Uniprot):Nr6a1
Mutagens:C104S
Chain IDs:B, D (auth: G)
Chain Length:84
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')
Chain IDs:C (auth: E)
Chain Length:16
Number of Molecules:1
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).
J. Mol. Biol. 428 4981 4992 (2016)
PMID: 27984042 DOI: 10.1016/j.jmb.2016.10.025

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures