1ED3 | pdb_00001ed3

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 (Depositor) 
  • R-Value Work: 
    0.222 (Depositor), 0.236 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 90.46 kDa 
  • Atom Count: 6,519 
  • Modeled Residue Count: 774 
  • Deposited Residue Count: 774 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
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Reference Sequence
Find similar proteins by:|  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
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UniProt GroupP07151
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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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.282 (Depositor) 
  • R-Value Work:  0.222 (Depositor), 0.236 (DCC) 
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

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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
  • Version 1.5: 2024-11-13
    Changes: Structure summary