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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Allogeneic H-2Kb MHC Class I MoleculeA [auth H],
F [auth I]		277Mus musculusMutation(s): 0 
Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01901
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

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)
Explore O08582 
Go to UniProtKB:  O08582
Entity Groups  
UniProt GroupO08582
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
KB5-C20 T-Cell receptor alpha-chainD [auth A],
I [auth D]		111Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P04214 
Go to UniProtKB:  P04214
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04214
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

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