› 5krb

X-ray diffraction
2.1Å resolution

GCNF DNA Binding Domain - Oct4 DR0 Complex

Released:
DOI: 10.2210/pdb5krb/pdb
PDB entry 5krb coloured by chain, front view.
PDB entry 5krb coloured by chain, side view.
PDB entry 5krb coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).
Weikum ER, Tuntland ML, Murphy MN, Ortlund EA
J Mol Biol 428 4981-4992 (2016)
PMID: 27984042

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118960 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Nuclear receptor subfamily 6 group A member 1 Chains: B, G
Molecule details ›
Chains: B, G
Length: 84 amino acids
Theoretical weight: 9.75 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q64249 (Residues: 72-155; Coverage: 17%)
Gene names: Gcnf, Nr6a1
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 5 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 16 nucleotides
Theoretical weight: 4.8 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 53.649Å b: 69.469Å c: 84.536Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.268
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

4 review citations

The nuclear receptor superfamily: A structural perspective.
Weikum et al. (2018)
3 more

1 mention without citation

A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).
Weikum et al. (2016)