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 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.219 

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This is version 2.0 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: 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 ...

    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.


    Related Citations: 
    • The three-dimentional structure of a T-cell antigen receptor ValphaVbeta heterodimer reveals a novel arrangement of the Vbeta domain
      Housset, D., Mazza, G., Gregoire, C., Piras, C., Malissen, B., Fontecilla-Camps, J.C.
      (1997) EMBO J 16: 4205
    • CRYSTAL STRUCTURE OF A T CELL RECEPTOR BOUND TO AN ALLOGENIC MHC MOLECULE
      Reiser, J.-B., Darnault, C., Guimezanes, A., Gregoire, C., Mosser, T., Schmitt-Verhulst, A.-M., Fontecilla-Camps, J.C., Malissen, B., Housset, D., Mazza, G.
      (2000) Nat Immunol 1: 291
    • IDENTIFICATION OF ENDOGENEOUS PEPTIDES RECOGNIZED BU IN VIVO OR IN VITRO GENERATED ALLOREACTIVE CTL: DISTINCT CHARACTERISTICS CORRELATED WITH CD8-DEPENDENCE
      Guimezanes, A., Barret-Wilt, G., Gulden-Thompson, P., Shabanowitz, J., Hunt, D., Schmitt-Verhulst, A.-M.
      (2001) Eur J Immunol 31: 421

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Allogeneic H-2Kb MHC Class I MoleculeA [auth H],
F [auth I]
277Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
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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Entity ID: 2
MoleculeChainsSequence 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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UniProt GroupO08582
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2 microglobulinC [auth L],
H [auth M]
99Mus musculusMutation(s): 0 
Gene Names: B2m
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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
KB5-C20 T-Cell receptor alpha-chainD [auth A],
I [auth D]
111Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence 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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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G70827FX
GlyCosmos:  G70827FX
GlyGen:  G70827FX
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth B],
M [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.219 
  • 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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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