› 6rti

X-ray diffraction
2.2Å resolution

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g

Released:
DOI: 10.2210/pdb6rti/pdb
PDB entry 6rti coloured by chain, front view.
PDB entry 6rti coloured by chain, side view.
PDB entry 6rti coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.
Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C
Nucleic Acids Res 48 11130-11145 (2020)
PMID: 32525981

Function and Biology Details

Reaction catalysed: 
Release of an unsubstituted, C-terminal glutamyl residue, typically from Ac-Asp-Glu or folylpoly-gamma-glutamates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170043 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (5 distinct):
Glutamate carboxypeptidase 2 Chain: A
Molecule details ›
Chain: A
Length: 707 amino acids
Theoretical weight: 79.61 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q04609 (Residues: 44-750; Coverage: 94%)
Gene names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA
Sequence domains:
Aptamer A9g, RNA (43-MER) Chain: X
Molecule details ›
Chain: X
Length: 43 nucleotides
Theoretical weight: 13.76 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
6 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 1 x CL
Ligand CA 1 x CA
Ligand G88 1 x G88
Ligand MPD 6 x MPD
Ligand ACT 1 x ACT
2 modified residues:
Ligand CFZ 12 x CFZ
Ligand UFT 10 x UFT

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P41212
Unit cell:
a: 121.096Å b: 121.096Å c: 216.271Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.217
Expression systems:
  • Drosophila melanogaster
  • Not provided

Quick links

Citations

5 review citations

Insights into Aptamer-Drug Delivery Systems against Prostate Cancer.
Wang et al. (2022)
4 more

2 mentions without citation

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.
Zhang et al. (2021)
1 more