2OL3 | pdb_00002ol3

crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.284 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?

Mazza, C.Auphan-Anezin, N.Gregoire, C.Guimezanes, A.Kellenberger, C.Roussel, A.Kearney, A.van der Merwe, P.A.Schmitt-Verhulst, A.M.Malissen, B.

(2007) EMBO J 26: 1972-1983

  • DOI: https://doi.org/10.1038/sj.emboj.7601605
  • Primary Citation of Related Structures:  
    2OL3

  • PubMed Abstract: 

    Binding degeneracy is thought to constitute a fundamental property of the T-cell antigen receptor (TCR), yet its structural basis is poorly understood. We determined the crystal structure of a complex involving the BM3.3 TCR and a peptide (pBM8) bound to the H-2K(bm8) major histocompatibility complex (MHC) molecule, and compared it with the structures of the BM3.3 TCR bound to H-2K(b) molecules loaded with two peptides that had a minimal level of primary sequence identity with pBM8. Our findings provide a refined structural view of the basis of BM3.3 TCR cross-reactivity and a structural explanation for the long-standing paradox that a TCR antigen-binding site can be both specific and degenerate. We also measured the thermodynamic features and biological penalties that incurred during cross-recognition. Our data illustrate the difficulty for a given TCR in adapting to distinct peptide-MHC surfaces while still maintaining affinities that result in functional in vivo responses. Therefore, when induction of protective effector T cells is used as the ultimate criteria for adaptive immunity, TCRs are probably much less degenerate than initially assumed.


  • Organizational Affiliation

    Centre d'Immunologie de Marseille-Luminy, Université de la Méditerrannée, 13288 Marseille Cedex 09, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BM3.3 T-CELL RECEPTOR ALPHA-CHAIN142Mus musculusMutation(s): 0 
UniProt
Find proteins for Q5R1F1 (Mus musculus)
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UniProt GroupQ5R1F1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BM3.3 T-CELL RECEPTOR BETA-CHAIN113Mus musculusMutation(s): 0 
UniProt
Find proteins for P04214 (Mus musculus)
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UniProt GroupP04214
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULEC [auth H]279Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
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UniProt GroupP01901
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth L]100Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NATURALLY PROCESSED OCTAPEPTIDE PBM8E [auth P]8N/AMutation(s): 0 
UniProt
Find proteins for Q91YE7 (Mus musculus)
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UniProt GroupQ91YE7
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.284 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.523α = 90
b = 102.523β = 90
c = 198.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary