1KJ3

Mhc Class I H-2Kb molecule complexed with pKB1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 

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 CD-8 DEPENDENCE
      Guimezanes, A.,Barret-Wilt, G.,Gulden-Thompson, P.,Shabanowitz, J.,Hunt, D.,Schmitt-Verhulst, A.-M.
      (2001) EUR.J.IMMUNOL. 31: 421
    • Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove
      Fremont, D.,Stura, E.,Matsumura, M.,Peterson, P.,Wilson, I.
      (1995) Proc.Natl.Acad.Sci.USA 92: 2479


    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
H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
H, I
279Mus 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.240α = 90.00
b = 90.630β = 111.51
c = 89.580γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
SCALAdata scaling
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: Version format compliance