› 6ryf

X-ray diffraction
1.72Å resolution

High-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide

Released:
DOI: 10.2210/pdb6ryf/pdb
PDB entry 6ryf coloured by chain, front view.
PDB entry 6ryf coloured by chain, side view.
PDB entry 6ryf coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1.
Giastas P, Mpakali A, Papakyriakou A, Lelis A, Kokkala P, Neu M, Rowland P, Liddle J, Georgiadis D, Stratikos E
Proc Natl Acad Sci U S A 116 26709-26716 (2019)
PMID: 31843903

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137931 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Endoplasmic reticulum aminopeptidase 1 Chain: A
Molecule details ›
Chain: A
Length: 894 amino acids
Theoretical weight: 102.21 KDa
Source organism: Homo sapiens
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: Q9NZ08 (Residues: 46-938; Coverage: 95%)
Gene names: APPILS, ARTS1, ERAP1, KIAA0525, UNQ584/PRO1154
Sequence domains:
Surface protein gp120 Chain: G
Molecule details ›
Chain: G
Length: 14 amino acids
Theoretical weight: 1.77 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04578 (Residues: 308-320; Coverage: 2%)
Gene name: env

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand ZN 1 x ZN
Ligand B3P 1 x B3P
Ligand EDO 21 x EDO
Ligand NA 4 x NA
Ligand PPI 1 x PPI
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Unit cell:
a: 57.693Å b: 117.157Å c: 146.598Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.201
Expression systems:
  • Spodoptera aff. frugiperda 1 BOLD-2017
  • Not provided

Quick links

Citations

3 review citations

HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole.
Kuiper et al. (2020)
2 more

3 mentions without citation

Phosphinic Peptides as Tool Compounds for the Study of Pharmacologically Relevant Zn-Metalloproteases.
Georgiadis et al. (2022)
2 more