› 4rbo

X-ray diffraction
3.3Å resolution

Crystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution

Released:
DOI: 10.2210/pdb4rbo/pdb
PDB entry 4rbo coloured by chain, front view.
PDB entry 4rbo coloured by chain, side view.
PDB entry 4rbo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.
Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ
Proc Natl Acad Sci U S A 112 4666-71 (2015)
PMID: 25825768

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-118089 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homeobox protein NANOG Chains: A, D
Molecule details ›
Chains: A, D
Length: 70 amino acids
Theoretical weight: 8.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H9S0 (Residues: 94-162; Coverage: 23%)
Gene name: NANOG
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P6522
Unit cell:
a: 215.603Å b: 215.603Å c: 42.269Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.235 0.268
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Molecular basis for the genome engagement by Sox proteins.
Hou et al. (2017)
7 more

6 mentions without citation

Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.
Hayashi et al. (2015)
5 more