3PGC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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 maintain a canonical orientation in the MHCII binding groove ...

    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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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainAD193Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chainBE199Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
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PHAROS  P01911
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen gamma chainCF15Homo sapiensMutation(s): 0 
Gene Names: CD74DHLAG
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
NIH Common Fund Data Resources
PHAROS  P04233
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download CCD File 
D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.146α = 90
b = 138.146β = 90
c = 104.52γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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