› 6pi7

X-ray diffraction
2.8Å resolution

Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide

Released:
DOI: 10.2210/pdb6pi7/pdb
PDB entry 6pi7 coloured by chain, front view.
PDB entry 6pi7 coloured by chain, side view.
PDB entry 6pi7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1.
Chen S, Zhang W, Min J, Liu K
Methods 175 72-78 (2020)
PMID: 31288074

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero trimer
PDBe Complex ID:
PDB-CPX-232168 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Tudor and KH domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 222 amino acids
Theoretical weight: 24.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2W6 (Residues: 305-525; Coverage: 39%)
Gene names: TDRD2, TDRKH
Sequence domains: Tudor domain
Uncharacterized protein Chains: B, E
Molecule details ›
Chains: B, E
Length: 226 amino acids
Theoretical weight: 24.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Fab antigen-binding fragment Chains: C, F
Molecule details ›
Chains: C, F
Length: 244 amino acids
Theoretical weight: 26.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Piwi-like protein 1 Chain: G
Molecule details ›
Chain: G
Length: 16 amino acids
Theoretical weight: 1.77 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q96J94 (Residues: 2-17; Coverage: 2%)
Gene names: HIWI, PIWIL1

Ligands and Environments

1 bound ligand:
Ligand UNX 5 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P63
Unit cell:
a: 148.099Å b: 148.099Å c: 168.026Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.19 0.206
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Effectors and effects of arginine methylation.
Wang et al. (2023)