4Z7I

Crystal structure of insulin regulated aminopeptidase in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing.

Mpakali, A.Saridakis, E.Harlos, K.Zhao, Y.Papakyriakou, A.Kokkala, P.Georgiadis, D.Stratikos, E.

(2015) J Immunol. 195: 2842-2851

  • DOI: 10.4049/jimmunol.1501103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understoo ...

    Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understood. In this work, we report the structure of insulin-regulated aminopeptidase, an enzyme that prepares antigenic epitopes for cross-presentation in dendritic cells, in complex with an antigenic peptide precursor analog. Insulin-regulated aminopeptidase is found in a semiclosed conformation with an extended internal cavity with limited access to the solvent. The N-terminal moiety of the peptide is located at the active site, positioned optimally for catalysis, whereas the C-terminal moiety of the peptide is stabilized along the extended internal cavity lodged between domains II and IV. Hydrophobic interactions and shape complementarity enhance peptide affinity beyond the catalytic site and support a limited selectivity model for antigenic peptide selection that may underlie the generation of complex immunopeptidomes.


    Organizational Affiliation

    National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucyl-cystinyl aminopeptidase
A, B
912Homo sapiensMutation(s): 0 
Gene Names: LNPEP (OTASE)
EC: 3.4.11.3
Find proteins for Q9UIQ6 (Homo sapiens)
Go to Gene View: LNPEP
Go to UniProtKB:  Q9UIQ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DG025 transition-state analogue enzyme inhibitor
C, D
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
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
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
4L8
Query on 4L8
C, D
L-peptide linkingC7 H15 N O2

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2X0
Query on 2X0
C, D
NON-POLYMERC9 H14 N O3 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.520α = 90.00
b = 256.350β = 111.58
c = 73.060γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
General Secretariat for Research & TechnologyGreeceERC-14
European UnionFP7 BioStruct-X 283570

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Derived calculations