1KJ2

Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


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 2.2 of the entry. See complete history


Literature

A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex.

Reiser, J.B.Gregoire, C.Darnault, C.Mosser, T.Guimezanes, A.Schmitt-Verhulst, A.M.Fontecilla-Camps, J.C.Mazza, G.Malissen, B.Housset, D.

(2002) Immunity 16: 345-354

  • DOI: https://doi.org/10.1016/s1074-7613(02)00288-1
  • Primary Citation of Related Structures:  
    1KJ2, 1KJ3

  • PubMed Abstract: 

    The elongated complementary-determining region (CDR) 3beta found in the unliganded KB5-C20 TCR protrudes from the antigen binding site and prevents its docking onto the peptide/MHC (pMHC) surface according to a canonical diagonal orientation. We now present the crystal structure of a complex involving the KB5-C20 TCR and an octapeptide bound to the allogeneic H-2K(b) MHC class I molecule. This structure reveals how a tremendously large CDR3beta conformational change allows the KB5-C20 TCR to adapt to the rather constrained pMHC surface and achieve a diagonal docking mode. This extreme case of induced fit also shows that TCR plasticity is primarily restricted to CDR3 loops and does not propagate away from the antigen binding site.


  • Organizational Affiliation

    Laboratoire de Cristallographie et Cristallogénèse des Protéines, Institut de Biologie Structurale J.-P. Ebel, CEA-CNRS-UJF, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allogeneic H-2Kb MHC Class I MoleculeA [auth H],
F [auth I]
277Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
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Go to UniProtKB:  P01901
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UniProt GroupP01901
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Naturally processed octapeptide PKB1B [auth P],
G [auth Q]
8N/AMutation(s): 0 
UniProt
Find proteins for O08582 (Mus musculus)
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Go to UniProtKB:  O08582
Entity Groups  
UniProt GroupO08582
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 microglobulinC [auth L],
H [auth M]
99Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
KB5-C20 T-Cell receptor alpha-chainD [auth A],
I [auth D]
111Mus musculusMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
KB5-C20 T-Cell receptor beta-chainE [auth B],
J [auth E]
117Mus musculusMutation(s): 0 
UniProt
Find proteins for P04214 (Mus musculus)
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Go to UniProtKB:  P04214
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UniProt GroupP04214
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04214-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth C]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G70827FX
GlyCosmos:  G70827FX
GlyGen:  G70827FX
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.2α = 90
b = 77.92β = 108.23
c = 132.96γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



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: 2002-03-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary