1ED3

CRYSTAL STRUCTURE OF RAT MINOR HISTOCOMPATIBILITY ANTIGEN COMPLEX RT1-AA/MTF-E.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa.

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

(2001) Immunity 14: 81-92

  • DOI: https://doi.org/10.1016/s1074-7613(01)00091-7
  • Primary Citation of Related Structures:  
    1ED3

  • PubMed Abstract: 

    The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. The antigenic structure of MTF-E was unpredictable due to its extraordinary length and two arginines that could serve as potential anchor residues. The crystal structure of RT1-Aa-MTF-E at 2.55 A shows that both peptide termini are anchored, as in other class I molecules, but the central residues in two independent pMHC complexes adopt completely different bulged conformations based on local environment. The MTF-E epitope is fully exposed within the putative T cell receptor (TCR) footprint. The flexibility demonstrated by the MTF-E structures illustrates how different TCRs may be raised against chemically identical, but structurally dissimilar, pMHC complexes.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
A, D
275Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P16391 (Rattus norvegicus)
Explore P16391 
Go to UniProtKB:  P16391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16391
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-2-MICROGLOBULIN
B, E
99Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P07151 (Rattus norvegicus)
Explore P07151 
Go to UniProtKB:  P07151
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07151
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDE MTF-E (13N3E)
C, F
13N/AMutation(s): 0 
UniProt
Find proteins for P05504 (Rattus norvegicus)
Explore P05504 
Go to UniProtKB:  P05504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05504
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.95α = 90
b = 90.72β = 90
c = 117.41γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-28
    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: 2018-01-24
    Changes: Database references
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Refinement description