3RJO

Crystal Structure of ERAP1 Peptide Binding Domain

• PDB DOI: https://doi.org/10.2210/pdb3RJO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2011-12-21 
• Deposition Author(s): Guo, H.-C., Lakshminarasimhan, D., Gandhi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.192 
• R-Value Observed: 0.196 

Literature

Structural insights into the molecular ruler mechanism of the endoplasmic reticulum aminopeptidase ERAP1.

Gandhi, A., Lakshminarasimhan, D., Sun, Y., Guo, H.C.

(2011) Sci Rep 1: 186-186

• PubMed: 22355701 
• DOI: https://doi.org/10.1038/srep00186
• Primary Citation of Related Structures:  
  3RJO


• PubMed Abstract: 
  

  Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an essential component of the immune system, because it trims peptide precursors and generates the N--restricted epitopes. To examine ERAP1's unique properties of length- and sequence-dependent processing of antigen precursors, we report a 2.3 Å resolution complex structure of the ERAP1 regulatory domain. Our study reveals a binding conformation of ERAP1 to the carboxyl terminus of a peptide, and thus provides direct evidence for the molecular ruler mechanism.

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Organizational Affiliation: 

Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.84 kDa 
• Atom Count: 3,492 
• Modelled Residue Count: 408 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum aminopeptidase 1	A	419	Homo sapiens	Mutation(s): 0  Gene Names: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ08 (Homo sapiens) Explore Q9NZ08  Go to UniProtKB:  Q9NZ08
PHAROS:  Q9NZ08 GTEx:  ENSG00000164307

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.192 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 67.31	β = 110.25
c = 65.92	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Guo, H.-C., Lakshminarasimhan, D., Gandhi, A.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references