3TFK

42F3-p4B10/H2-Ld


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.

Adams, J.J.Narayanan, S.Liu, B.Birnbaum, M.E.Kruse, A.C.Bowerman, N.A.Chen, W.Levin, A.M.Connolly, J.M.Zhu, C.Kranz, D.M.Garcia, K.C.

(2011) Immunity 35: 681-693

  • DOI: 10.1016/j.immuni.2011.09.013
  • Primary Citation of Related Structures:  
    3TF7, 3TFK, 3TJH, 3TPU

  • PubMed Abstract: 
  • T cell receptor (TCR) engagement of peptide-major histocompatibility complex (pMHC) is essential to adaptive immunity, but it is unknown whether TCR signaling responses are influenced by the binding topology of the TCR-peptide-MHC complex. We develop ...

    T cell receptor (TCR) engagement of peptide-major histocompatibility complex (pMHC) is essential to adaptive immunity, but it is unknown whether TCR signaling responses are influenced by the binding topology of the TCR-peptide-MHC complex. We developed yeast-displayed pMHC libraries that enabled us to identify new peptide sequences reactive with a single TCR. Structural analysis showed that four peptides bound to the TCR with distinct 3D and 2D affinities using entirely different binding chemistries. Three of the peptides that shared a common docking mode, where key TCR-MHC germline interactions are preserved, induced TCR signaling. The fourth peptide failed to induce signaling and was recognized in a substantially different TCR-MHC binding mode that apparently exceeded geometric tolerances compatible with signaling. We suggest that the stereotypical TCR-MHC docking paradigm evolved from productive signaling geometries and that TCR signaling can be modulated by peptides that are recognized in alternative TCR-pMHC binding orientations.


    Organizational Affiliation

    Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H2-Ld SBM2A180Mus musculusMutation(s): 0 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Explore P01897 
Go to UniProtKB:  P01897
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
p4B10 peptideB9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 alphaC212Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 betaD243Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download CCD File 
D
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.09α = 90
b = 102.09β = 90
c = 323.081γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Database references