4X5X

HLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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
  • Structures With Same Primary Citation

  • 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 Universität 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, C
193Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-1 beta chain
B, D
229Homo sapiensMutation(s): 1 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.821α = 90
b = 86.467β = 103.96
c = 94.11γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XSCALEdata scaling
XSCALEdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyFR-1325/11-1
DFGGermanySFB 765
DFGGermany854
DFGGermany958

Revision History 

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