4X5W

HLA-DR1 with CLIP102-120(M107W)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

MHC class II complexes sample intermediate states along the peptide exchange pathway.

Wieczorek, M.Sticht, J.Stolzenberg, S.Gunther, S.Wehmeyer, C.El Habre, Z.Alvaro-Benito, M.Noe, F.Freund, C.

(2016) Nat Commun 7: 13224-13224

  • DOI: 10.1038/ncomms13224
  • Primary Citation of Related Structures:  4X5X

  • PubMed Abstract: 
  • The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Ma ...

    The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Markov modelling analysis of an aggregate of 275 microseconds molecular dynamics simulations, we reveal that a stable pMHCII spontaneously samples intermediate conformations relevant for peptide exchange. More specifically, we observe two major peptide exchange pathways: the kinetic stability of a pMHCII's ground state defines its propensity for intrinsic peptide exchange, while the population of a rare, intermediate conformation correlates with the propensity of the HLA-DM-catalysed pathway. Helix-destabilizing mutants designed based on our model shift the exchange behaviour towards the HLA-DM-catalysed pathway and further allow us to conceptualize how allelic variation can shape an individual's MHC restricted immune response.


    Organizational Affiliation

    Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universit├Ąt Berlin, Thielallee 63, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
193Homo sapiensGene 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
199Homo sapiensGene 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 II histocompatibility antigen gamma chain
C
19Homo sapiensGene 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: 1.34 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.146 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.775α = 90.00
b = 90.851β = 90.00
c = 138.793γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XSCALEdata reduction
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
DFGGermanyFR-1325/11-1
DFGGermanySFB 765
DFGGermanySFB 854
DFGGermanySFB 958

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references