4P2O

Crystal structure of the 2B4 TCR in complex with 2A/I-Ek


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.603 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

Literature

Deconstructing the Peptide-MHC Specificity of T Cell Recognition.

Birnbaum, M.E.Mendoza, J.L.Sethi, D.K.Dong, S.Glanville, J.Dobbins, J.Ozkan, E.Davis, M.M.Wucherpfennig, K.W.Garcia, K.C.

(2014) Cell 157: 1073-1087

  • DOI: 10.1016/j.cell.2014.03.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and ...

    In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.


    Organizational Affiliation

    Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: kcgarcia@stanford.edu.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, E-K alpha chain
A
204Mus musculusMutation(s): 0 
Find proteins for P04224 (Mus musculus)
Go to UniProtKB:  P04224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II E-beta-k
B
236Mus musculusMutation(s): 0 
Gene Names: H2-Eb1
Find proteins for Q31163 (Mus musculus)
Go to UniProtKB:  Q31163
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
2B4 T-cell receptor alpha chain
C
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
2B4 T-cell receptor beta chain
D
255N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
2A peptide
P
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.603 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 239.936α = 90.00
b = 60.176β = 104.33
c = 78.359γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references
  • Version 1.3: 2015-02-25
    Type: Derived calculations
  • Version 2.0: 2017-09-20
    Type: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-01
    Type: Author supporting evidence
  • Version 2.2: 2019-12-25
    Type: Author supporting evidence, Data collection