5KSU

Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides.

Nguyen, T.B.Jayaraman, P.Bergseng, E.Madhusudhan, M.S.Kim, C.Y.Sollid, L.M.

(2017) J. Biol. Chem. 292: 9218-9228

  • DOI: 10.1074/jbc.M117.785139
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human leukocyte antigen (HLA)-DQ2.5 ( <i>DQA1 </i>* <i>05/DQB1 </i>* <i>02 </i>) is a class-II major histocompatibility complex protein associated with both type 1 diabetes and celiac disease. One unusual feature of DQ2.5 is its high class-II-associa ...

    Human leukocyte antigen (HLA)-DQ2.5 ( DQA1 * 05/DQB1 * 02 ) is a class-II major histocompatibility complex protein associated with both type 1 diabetes and celiac disease. One unusual feature of DQ2.5 is its high class-II-associated invariant chain peptide (CLIP) content. Moreover, HLA-DQ2.5 preferentially binds the non-canonical CLIP2 over the canonical CLIP1. To better understand the structural basis of HLA-DQ2.5's unusual CLIP association characteristics, better insight into the HLA-DQ2.5·CLIP complex structures is required. To this end, we determined the X-ray crystal structure of the HLA-DQ2.5· CLIP1 and HLA-DQ2.5·CLIP2 complexes at 2.73 and 2.20 Å, respectively. We found that HLA-DQ2.5 has an unusually large P4 pocket and a positively charged peptide-binding groove that together promote preferential binding of CLIP2 over CLIP1. An α9-α22-α24-α31-β86-β90 hydrogen bond network located at the bottom of the peptide-binding groove, spanning from the P1 to P4 pockets, renders the residues in this region relatively immobile. This hydrogen bond network, along with a deletion mutation at α53, may lead to HLA-DM insensitivity in HLA-DQ2.5. A molecular dynamics simulation experiment reported here and recent biochemical studies by others support this hypothesis. The diminished HLA-DM sensitivity is the likely reason for the CLIP-rich phenotype of HLA-DQ2.5.


    Organizational Affiliation

    the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway l.m.sollid@medisin.uio.no.,the Indian Institute of Science Education and Research, Pune 411008, India, and.,Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute, National University of Singapore, 117456 Singapore, Singapore.,the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,From the Department of Chemistry and ckim7@utep.edu.,the Bioinformatics Institute, Singapore 138671, Singapore.,the Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.,School of Pharmacy, University of Texas at El Paso, El Paso, Texas 79968.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DQ alpha 1 chain
A, D
199Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for P01909 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  P01909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-beta-1
B, E
204Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for Q5Y7D3 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  Q5Y7D3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen gamma chain
C, F
15Homo sapiensMutation(s): 0 
Gene Names: CD74 (DHLAG)
Find proteins for P04233 (Homo sapiens)
Go to Gene View: CD74
Go to UniProtKB:  P04233
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.860α = 90.00
b = 69.210β = 110.29
c = 146.690γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references