3QNF

Crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 ERAP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming.

Kochan, G.Krojer, T.Harvey, D.Fischer, R.Chen, L.Vollmar, M.von Delft, F.Kavanagh, K.L.Brown, M.A.Bowness, P.Wordsworth, P.Kessler, B.M.Oppermann, U.

(2011) Proc.Natl.Acad.Sci.USA 108: 7745-7750

  • DOI: 10.1073/pnas.1101262108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endoplasmatic reticulum aminopeptidase 1 (ERAP1) is a multifunctional enzyme involved in trimming of peptides to an optimal length for presentation by major histocompatibility complex (MHC) class I molecules. Polymorphisms in ERAP1 have been associat ...

    Endoplasmatic reticulum aminopeptidase 1 (ERAP1) is a multifunctional enzyme involved in trimming of peptides to an optimal length for presentation by major histocompatibility complex (MHC) class I molecules. Polymorphisms in ERAP1 have been associated with chronic inflammatory diseases, including ankylosing spondylitis (AS) and psoriasis, and subsequent in vitro enzyme studies suggest distinct catalytic properties of ERAP1 variants. To understand structure-activity relationships of this enzyme we determined crystal structures in open and closed states of human ERAP1, which provide the first snapshots along a catalytic path. ERAP1 is a zinc-metallopeptidase with typical H-E-X-X-H-(X)(18)-E zinc binding and G-A-M-E-N motifs characteristic for members of the gluzincin protease family. The structures reveal extensive domain movements, including an active site closure as well as three different open conformations, thus providing insights into the catalytic cycle. A K(528)R mutant strongly associated with AS in GWAS studies shows significantly altered peptide processing characteristics, which are possibly related to impaired interdomain interactions.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmic reticulum aminopeptidase 1
A, B, C
954Homo sapiensMutation(s): 0 
Gene Names: ERAP1 (APPILS, ARTS1, KIAA0525)
EC: 3.4.11.-
Find proteins for Q9NZ08 (Homo sapiens)
Go to Gene View: ERAP1
Go to UniProtKB:  Q9NZ08
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.246α = 90.00
b = 132.816β = 90.00
c = 233.687γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
GDAdata collection
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-31
    Type: Structure summary