6BJ8

TCR55 in complex with Pep20/HLA-B35

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.

Sibener, L.V., Fernandes, R.A., Kolawole, E.M., Carbone, C.B., Liu, F., McAffee, D., Birnbaum, M.E., Yang, X., Su, L.F., Yu, W., Dong, S., Gee, M.H., Jude, K.M., Davis, M.M., Groves, J.T., Goddard III, W.A., Heath, J.R., Evavold, B.D., Vale, R.D., Garcia, K.C.

(2018) Cell 174: 672-687.e27

  • DOI: 10.1016/j.cell.2018.06.017
  • Primary Citation of Related Structures:  
    6BJ2, 6BJ3, 6BJ8

  • PubMed Abstract: 

    • TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human T cell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding ...

    TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human T cell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding. Analysis of 3D affinity, 2D dwell time, and crystal structures of stimulatory versus non-stimulatory TCR-pMHC interactions failed to account for their different signaling outcomes. Using yeast pMHC display, we identified peptide agonists of a formerly non-responsive TCR. Single-molecule force measurements demonstrated the emergence of catch bonds in the activating TCR-pMHC interactions, correlating with exclusion of CD45 from the TCR-APC contact site. Molecular dynamics simulations of TCR-pMHC disengagement distinguished agonist from non-agonist ligands based on the acquisition of catch bonds within the TCR-pMHC interface. The isolation of catch bonds as a parameter mediating the coupling of TCR binding and signaling has important implications for TCR and antigen engineering for immunotherapy.

    Organizational Affiliation: 

    Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; 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
HLA class I histocompatibility antigen, B-35 alpha chainA276Homo sapiensMutation(s): 0 
Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
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Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 55 alpha chainC [auth D]204Homo sapiensMutation(s): 1 
Gene Names: TRA@
UniProt
Find proteins for Q6IRV4 (Homo sapiens)
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Go to UniProtKB:  Q6IRV4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 55 beta chainD [auth H]242Homo sapiensMutation(s): 1 
Gene Names: B2M
UniProt
Find proteins for K7N5M4 (Homo sapiens)
Explore K7N5M4 
Go to UniProtKB:  K7N5M4
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEUE [auth C]9synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
JA [auth H], P [auth A], X [auth D], Y [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth H] , BA [auth H] , CA [auth H] , DA [auth H] , EA [auth H] , F [auth A] , FA [auth H] , G [auth A] , 
AA [auth H], BA [auth H], CA [auth H], DA [auth H], EA [auth H], F [auth A], FA [auth H], G [auth A], GA [auth H], H [auth A], HA [auth H], I [auth A], IA [auth H], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], T [auth D], U [auth D], V [auth D], W [auth D], Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/517 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.492α = 90
b = 61.698β = 104.87
c = 92.145γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI07290
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA216926-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI57229
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103867
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI096879
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS071518
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesA1091580
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA199090-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence