4P2R

Crystal structure of the 5cc7 TCR in complex with 5c1/I-Ek


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.6 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:  
    4P2O, 4P2Q, 4P2R

  • 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; 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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, E-K alpha chainAFKP204Mus musculusMutation(s): 0 
Find proteins for P04224 (Mus musculus)
Explore P04224 
Go to UniProtKB:  P04224
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II E-beta-kBGLQ212Mus musculusMutation(s): 0 
Gene Names: H2-Eb1
Find proteins for Q31163 (Mus musculus)
Explore Q31163 
Go to UniProtKB:  Q31163
NIH Common Fund Data Resources
IMPC  MGI:95901
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5c1 peptideCHMR13synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
5cc7 T-cell receptor alpha chainDINS205Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
5cc7 T-cell receptor beta chainEJOT266Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, G, K, L
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: 3.29 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.601α = 90
b = 101.867β = 94.89
c = 214.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2015-02-25
    Changes: Derived calculations
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.5: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary