Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.13 kDa 
• Atom Count: 3298 
• Residue Count: 394 
• Unique protein chains: 3

1KJM

TAP-A-associated rat MHC class I molecule

• DOI: 10.2210/pdb1KJM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-04 Released: 2002-12-18 
• Deposition Author(s): Rudolph, M.G., Stevens, J., Speir, J.A., Trowsdale, J., Butcher, G.W., Joly, E., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.268 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

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

• PubMed: 12470953 
• DOI: 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RT1 class I histocompatibility antigen, AA alpha chain, heavy chain	A	285	Rattus norvegicus	Mutation(s): 0
Find proteins for P16391 (Rattus norvegicus) Explore P16391  Go to UniProtKB:  P16391

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-2-Microglobulin	B	100	Rattus norvegicus	Mutation(s): 0  Gene Names: B2m
Find proteins for P07151 (Rattus norvegicus) Explore P07151  Go to UniProtKB:  P07151

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B6 Peptide	P	9	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.268 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.049	α = 90
b = 109.566	β = 90
c = 45.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-04 
• Released Date: 2002-12-18 
Deposition Author(s): Rudolph, M.G., Stevens, J., Speir, J.A., Trowsdale, J., Butcher, G.W., Joly, E., Wilson, I.A.

Revision History 

• 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: Advisory, Version format compliance