4OV5

Structure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide.

Yin, L.Trenh, P.Guce, A.Wieczorek, M.Lange, S.Sticht, J.Jiang, W.Bylsma, M.Mellins, E.D.Freund, C.Stern, L.J.

(2014) J.Biol.Chem. 289: 23449-23464

  • DOI: 10.1074/jbc.M114.585539

  • PubMed Abstract: 
  • HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides int ...

    HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides interacting nonoptimally in the P1 pocket exhibited low MHCII binding affinity and kinetic instability and were highly susceptible to HLA-DM-mediated peptide exchange. These changes were accompanied by conformational alterations detected by surface plasmon resonance, SDS resistance assay, antibody binding assay, gel filtration, dynamic light scattering, small angle x-ray scattering, and NMR spectroscopy. Surprisingly, all of those changes could be reversed by substitution of the P9 pocket anchor residue. Moreover, MHCII mutations outside the P1 pocket and the HLA-DM interaction site increased HLA-DM susceptibility. These results indicate that a dynamic MHCII conformational determinant rather than P1 pocket occupancy is the key factor determining susceptibility to HLA-DM-mediated peptide exchange and provide a molecular mechanism for HLA-DM to efficiently target unstable MHCII-peptide complexes for editing and exchange those for more stable ones.


    Organizational Affiliation

    From the Program in Immunology and Microbiology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, D, G, J, M, P
182Homo 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, H, K, N, Q
190Homo 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
HLA class I histocompatibility antigen, A-2 alpha chain
C, F, I, L, O, R
14Homo sapiensMutation(s): 2 
Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01892
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.955α = 90.00
b = 173.188β = 109.72
c = 96.484γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
CBASSdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references
  • Version 1.2: 2014-09-10
    Type: Database references