1KJM

TAP-A-associated rat MHC class I molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa
      Speir, J.A.,Stevens, J.S.,Joly, E.,Butcher, G.W.,Wilson, I.A.
      (2001) Immunity 14: 81


    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RT1 class I histocompatibility antigen, AA alpha chain, heavy chain
A
285Rattus norvegicusMutation(s): 0 
Find proteins for P16391 (Rattus norvegicus)
Go to UniProtKB:  P16391
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
beta-2-Microglobulin
B
100Rattus norvegicusMutation(s): 0 
Gene Names: B2m
Find proteins for P07151 (Rattus norvegicus)
Go to UniProtKB:  P07151
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
B6 Peptide
P
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.049α = 90.00
b = 109.566β = 90.00
c = 45.300γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance