6RPB

Crystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex.

Coles, C.H., Mulvaney, R.M., Malla, S., Walker, A., Smith, K.J., Lloyd, A., Lowe, K.L., McCully, M.L., Martinez Hague, R., Aleksic, M., Harper, J., Paston, S.J., Donnellan, Z., Chester, F., Wiederhold, K., Robinson, R.A., Knox, A., Stacey, A.R., Dukes, J., Baston, E., Griffin, S., Jakobsen, B.K., Vuidepot, A., Harper, S.

(2020) J Immunol 204: 1943-1953

  • DOI: 10.4049/jimmunol.1900915
  • Primary Citation of Related Structures:  
    6RPA, 6RPB, 6RP9

  • PubMed Abstract: 

    • The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using ...

    The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1 157-165 -HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.

    Organizational Affiliation: 

    Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and Stephen.Harper@immunocore.com bent.jakobsen@immunocore.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA, F, K, P277Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, G, L, Q100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Heteroclitic NY-ESO-1 157-165 peptideC, H, M, R9Homo sapiensMutation(s): 0 
Gene Names: CTAG1A, CTAG, CTAG1, ESO1, LAGE2, LAGE2A, CTAG1B, LAGE2B
Find proteins for P78358 (Homo sapiens)
Explore P78358 
Go to UniProtKB:  P78358
NIH Common Fund Data Resources
PHAROS  P78358
GTEx  ENSG00000184033GTEx  ENSG00000268651
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha chainD, I, N, S206Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor beta chainE, J, O, T244Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.342α = 93.02
b = 77.134β = 93.45
c = 184.632γ = 108.16
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2020-04-08
    Changes: Database references