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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  

  • 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 ...

    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: 
    • 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
    • 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

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Allogeneic H-2Kb MHC Class I Molecule
H, I
277Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Naturally processed octapeptide PKB1
P, Q
8Mus musculusMutation(s): 0 
Gene Names: Gtpbp1 (Gtpbp)
Find proteins for O08582 (Mus musculus)
Go to UniProtKB:  O08582
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Beta-2 microglobulin
L, M
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
KB5-C20 T-Cell receptor alpha-chain
A, D
111N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
KB5-C20 T-Cell receptor beta-chain
B, E
117Mus musculusMutation(s): 0 
Find proteins for P04214 (Mus musculus)
Go to UniProtKB:  P04214
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL
Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA
Download SDF File 
Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.200α = 90.00
b = 77.920β = 108.23
c = 132.960γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
AMoREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance