3TF7

42F3 QL9/H2-Ld complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

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 developed yeast-displayed pMHC libraries that enabled us to identify new peptide sequences reactive with a single TCR ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H2-Ld SBM2D [auth A],
A [auth E]		180Mus musculusMutation(s): 0 
Gene Names: H2-L
UniProt
Find proteins for P01897 (Mus musculus)
Explore P01897 
Go to UniProtKB:  P01897
Entity Groups  
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UniProt GroupP01897
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
QL9 peptide (QLSPFPFDL)E [auth B],
B [auth F]		9Mus musculusMutation(s): 0 
Gene Names: Ogdh, Kiaa4192
EC: 1.2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q60597 (Mus musculus)
Explore Q60597 
Go to UniProtKB:  Q60597
IMPC:  MGI:1098267
Entity Groups  
UniProt GroupQ60597
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)C,
F [auth G],
G [auth I],
H [auth K]		256Mus musculusMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth C],
J [auth G]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.487α = 90
b = 109.793β = 90
c = 213.59γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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