4I5B

Structure of human MHC class II protein HLA-DR1 carrying an influenza hemagglutinin peptide partially filling the binding groove


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Disruption of hydrogen bonds between major histocompatibility complex class II and the peptide N-terminus is not sufficient to form a human leukocyte antigen-DM receptive state of major histocompatibility complex class II.

Schulze, M.S.Anders, A.K.Sethi, D.K.Call, M.J.

(2013) Plos One 8: e69228-e69228

  • DOI: 10.1371/journal.pone.0069228

  • PubMed Abstract: 
  • Peptide presentation by MHC class II is of critical importance to the function of CD4+ T cells. HLA-DM resides in the endosomal pathway and edits the peptide repertoire of newly synthesized MHC class II molecules before they are exported to the cell ...

    Peptide presentation by MHC class II is of critical importance to the function of CD4+ T cells. HLA-DM resides in the endosomal pathway and edits the peptide repertoire of newly synthesized MHC class II molecules before they are exported to the cell surface. HLA-DM ensures MHC class II molecules bind high affinity peptides by targeting unstable MHC class II:peptide complexes for peptide exchange. Research over the past decade has implicated the peptide N-terminus in modulating the ability of HLA-DM to target a given MHC class II:peptide combination. In particular, attention has been focused on both the hydrogen bonds between MHC class II and peptide, and the occupancy of the P1 anchor pocket. We sought to solve the crystal structure of a HLA-DR1 molecule containing a truncated hemagglutinin peptide missing three N-terminal residues compared to the full-length sequence (residues 306-318) to determine the nature of the MHC class II:peptide species that binds HLA-DM. Here we present structural evidence that HLA-DR1 that is loaded with a peptide truncated to the P1 anchor residue such that it cannot make select hydrogen bonds with the peptide N-terminus, adopts the same conformation as molecules loaded with full-length peptide. HLA-DR1:peptide combinations that were unable to engage up to four key hydrogen bonds were also unable to bind HLA-DM, while those truncated to the P2 residue bound well. These results indicate that the conformational changes in MHC class II molecules that are recognized by HLA-DM occur after disengagement of the P1 anchor residue.


    Organizational Affiliation

    Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, D
187Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-1 beta chain
B, E
192Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P04229
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
truncated hemagglutinin peptide
C, F
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.811α = 90.00
b = 111.381β = 90.00
c = 211.544γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-28 
  • Released Date: 2013-12-04 
  • Deposition Author(s): Schulze, M.-S.E.D.

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references