3QXA

HLA-DR1 bound with CLIP peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Conformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange.

Painter, C.A., Negroni, M.P., Kellersberger, K.A., Zavala-Ruiz, Z., Evans, J.E., Stern, L.J.

(2011) Proc Natl Acad Sci U S A 108: 19329-19334

  • DOI: 10.1073/pnas.1108074108
  • Primary Citation of Related Structures:  
    3QXD, 3QXA

  • PubMed Abstract: 

    • HLA-DM is required for efficient peptide exchange on class II MHC molecules, but its mechanism of action is controversial. We trapped an intermediate state of class II MHC HLA-DR1 by substitution of αF54, resulting in a protein with increased HLA-DM bind ...

    HLA-DM is required for efficient peptide exchange on class II MHC molecules, but its mechanism of action is controversial. We trapped an intermediate state of class II MHC HLA-DR1 by substitution of αF54, resulting in a protein with increased HLA-DM binding affinity, weakened MHC-peptide hydrogen bonding as measured by hydrogen-deuterium exchange mass spectrometry, and increased susceptibility to DM-mediated peptide exchange. Structural analysis revealed a set of concerted conformational alterations at the N-terminal end of the peptide-binding site. These results suggest that interaction with HLA-DM is driven by a conformational change of the MHC II protein in the region of the α-subunit 3(10) helix and adjacent extended strand region, and provide a model for the mechanism of DM-mediated peptide exchange.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 10655, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain A, D182Homo sapiensMutation(s): 0 
Gene Names: HLA-DR1, HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903
GTEx:  ENSG00000204287
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chain B, E190Homo sapiensMutation(s): 0 
Gene Names: HLA-DR1, HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS:  P01911
GTEx:  ENSG00000196126
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen gamma chain peptide C, F15Homo sapiensMutation(s): 0 
Gene Names: CD74, DHLAG
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
NIH Common Fund Data Resources
PHAROS:  P04233
GTEx:  ENSG00000019582
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.296α = 90
b = 95.887β = 90
c = 151.573γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2011-12-14
    Changes: Database references