1KJV

TAP-B-associated rat MHC class I molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B.

Rudolph, M.G.Stevens, J.Speir, J.A.Trowsdale, J.Butcher, G.W.Joly, E.Wilson, I.A.

(2002) J Mol Biol 324: 975-990

  • DOI: https://doi.org/10.1016/s0022-2836(02)01095-1
  • Primary Citation of Related Structures:  
    1KJM, 1KJV

  • PubMed Abstract: 

    Antigenic peptides are loaded onto class I MHC molecules in the endoplasmic reticulum (ER) by a complex consisting of the MHC class I heavy chain, beta(2)-microglobulin, calreticulin, tapasin, Erp57 (ER60) and the transporter associated with antigen processing (TAP). While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, that are present in different inbred strains. Each TAP delivers a different spectrum of peptides and is associated genetically with distinct subsets of MHC class Ia alleles, but the molecular basis for the conservation (or co-evolution) of the two transporter alleles is unknown. We have determined the crystal structures of a representative of each MHC subset, viz RT1-A(a) and RT1-A1(c), in association with high-affinity nonamer peptides. The structures reveal how the chemical properties of the two different rat MHC F-pockets match those of the corresponding C termini of the peptides, corroborating biochemical data on the rates of peptide-MHC complex assembly. An unusual sequence in RT1-A1(c) leads to a major deviation from the highly conserved beta(3)/alpha(1) loop (residues 40-59) conformation in mouse and human MHC class I structures. This loop change contributes to profound changes in the shape of the A-pocket in the peptide-binding groove and may explain the function of RT1-A1(c) as an inhibitory natural killer cell ligand.


  • Organizational Affiliation

    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mature alpha chain of major histocompatibility complex class I antigen (HEAVY CHAIN)284Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q95565 (Rattus norvegicus)
Explore Q95565 
Go to UniProtKB:  Q95565
Entity Groups  
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UniProt GroupQ95565
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
beta-2-microglobulin100Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P07151 (Rattus norvegicus)
Explore P07151 
Go to UniProtKB:  P07151
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UniProt GroupP07151
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
peptide NPRC [auth P]9N/AMutation(s): 0 
UniProt
Find proteins for Q9JJP9 (Rattus norvegicus)
Explore Q9JJP9 
Go to UniProtKB:  Q9JJP9
Entity Groups  
UniProt GroupQ9JJP9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.397α = 90
b = 50.522β = 90
c = 200.073γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description