3PGD

Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Bidirectional binding of invariant chain peptides to an MHC class II molecule.

Gunther, S., Schlundt, A., Sticht, J., Roske, Y., Heinemann, U., Wiesmuller, K.H., Jung, G., Falk, K., Rotzschke, O., Freund, C.

(2010) Proc Natl Acad Sci U S A 107: 22219-22224

  • DOI: 10.1073/pnas.1014708107
  • Primary Citation of Related Structures:  
    3PDO, 3PGC, 3PGD

  • PubMed Abstract: 

    • T-cell recognition of peptides bound to MHC class II (MHCII) molecules is a central event in cell-mediated adaptive immunity. The current paradigm holds that prebound class II-associated invariant chain peptides (CLIP) and all subsequent antigens maintai ...

    T-cell recognition of peptides bound to MHC class II (MHCII) molecules is a central event in cell-mediated adaptive immunity. The current paradigm holds that prebound class II-associated invariant chain peptides (CLIP) and all subsequent antigens maintain a canonical orientation in the MHCII binding groove. Here we provide evidence for MHCII-bound CLIP inversion. NMR spectroscopy demonstrates that the interconversion from the canonical to the inverse alignment is a dynamic process, and X-ray crystallography shows that conserved MHC residues form a hydrogen bond network with the peptide backbone in both orientations. The natural catalyst HLA-DM accelerates peptide reorientation and the exchange of either canonically or inversely bound CLIP against antigenic peptide. Thus, noncanonical MHC-CLIP displays the hallmarks of a structurally and functionally intact antigen-presenting complex.

    Organizational Affiliation: 

    Leibniz-Institute for Molecular Pharmacology and Freie Universität Berlin, 13125 Berlin, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain A, D193Homo sapiensMutation(s): 0 
Gene Names: 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, E199Homo sapiensMutation(s): 0 
Gene Names: 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 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: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.449α = 90
b = 94.449β = 90
c = 275.535γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance