› 5v3g

X-ray diffraction
2.42Å resolution

PRDM9-allele-C ZnF8-13

Released:
DOI: 10.2210/pdb5v3g/pdb
PDB entry 5v3g coloured by chain, front view.
PDB entry 5v3g coloured by chain, side view.
PDB entry 5v3g coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence.
Patel A, Zhang X, Blumenthal RM, Cheng X
J Biol Chem 292 15994-16002 (2017)
PMID: 28801461

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112966 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
C2H2-type domain-containing protein Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 174 amino acids
Theoretical weight: 20.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D9IWL3 (Residues: 301-470; Coverage: 34%)
Gene name: PRMD9
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 21 nucleotides
Theoretical weight: 6.4 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 13 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 63.151Å b: 123.778Å c: 70.2Å
α: 90° β: 116.07° γ: 90°
R-values:
R R work R free
0.176 0.173 0.225
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

PRDM9, a driver of the genetic map.
Grey et al. (2018)
3 other articles

7 mentions without citation

A variant in human AIOLOS impairs adaptive immunity by interfering with IKAROS.
Yamashita et al. (2021)
6 more