5OPI

Crystal structure of the TAPBPR-MHC I peptide editing complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the TAPBPR-MHC I complex defines the mechanism of peptide loading and editing.

Thomas, C.Tampe, R.

(2017) Science 358: 1060-1064

  • DOI: https://doi.org/10.1126/science.aao6001
  • Primary Citation of Related Structures:  
    5OPI

  • PubMed Abstract: 

    Adaptive immunity is shaped by a selection of peptides presented on major histocompatibility complex class I (MHC I) molecules. The chaperones Tapasin (Tsn) and TAP-binding protein-related (TAPBPR) facilitate MHC I peptide loading and high-affinity epitope selection. Despite the pivotal role of Tsn and TAPBPR in controlling the hierarchical immune response, their catalytic mechanism remains unknown. Here, we present the x-ray structure of the TAPBPR-MHC I complex, which delineates the central step of catalysis. TAPBPR functions as peptide selector by remodeling the MHC I α2-1-helix region, stabilizing the empty binding groove, and inserting a loop into the groove that interferes with peptide binding. The complex explains how mutations in MHC I-specific chaperones cause defects in antigen processing and suggests a unifying mechanism of peptide proofreading.


  • Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany. c.thomas@em.uni-frankfurt.de tampe@em.uni-frankfurt.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain279Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups  
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UniProt GroupP01899
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
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UniProt GroupP61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TAP binding protein-like variant373Homo sapiensMutation(s): 2 
UniProt
Find proteins for Q53GH5 (Homo sapiens)
Explore Q53GH5 
Go to UniProtKB:  Q53GH5
Entity Groups  
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UniProt GroupQ53GH5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.04α = 90
b = 205.04β = 90
c = 121.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 807/P16

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description