› 5l0m

X-ray diffraction
2.2Å resolution

hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex

Released:
DOI: 10.2210/pdb5l0m/pdb
PDB entry 5l0m coloured by chain, front view.
PDB entry 5l0m coloured by chain, side view.
PDB entry 5l0m coloured by chain, top view.
Source organisms:
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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118973 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Nuclear receptor subfamily 5 group A member 2 Chain: A
Molecule details ›
Chain: A
Length: 112 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00482 (Residues: 79-187; Coverage: 20%)
Gene names: B1F, CPF, FTF, NR5A2
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.6 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43
Unit cell:
a: 40.931Å b: 40.931Å c: 105.055Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.154 0.197
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Networks of Transcription Factors for Oct4 Expression in Mice.
Li YQ. (2017)
2 more

3 mentions without citation

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