8ES9

CryoEM structure of PN45428 TCR-CD3 in complex with HLA-A2 MAGEA4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM.

Saotome, K.Dudgeon, D.Colotti, K.Moore, M.J.Jones, J.Zhou, Y.Rafique, A.Yancopoulos, G.D.Murphy, A.J.Lin, J.C.Olson, W.C.Franklin, M.C.

(2023) Nat Commun 14: 2401-2401

  • DOI: https://doi.org/10.1038/s41467-023-37532-7
  • Primary Citation of Related Structures:  
    8ES7, 8ES8, 8ES9, 8ESA, 8ESB

  • PubMed Abstract: 

    The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.


  • Organizational Affiliation

    Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA. kei.saotome@regeneron.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PN45428 TCR alpha chain274Homo sapiensMutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PN45428 TCR beta chain320Homo sapiensMutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainC [auth Z],
D [auth Y]
173Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainE [auth D]174Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
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Find proteins for P04234 (Homo sapiens)
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PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04234-1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainF,
H [auth E]
211Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
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Find proteins for P07766 (Homo sapiens)
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PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chain185Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
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Find proteins for P09693 (Homo sapiens)
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PHAROS:  P09693
GTEx:  ENSG00000160654 
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UniProt GroupP09693
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P09693-1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigenI [auth N]277Homo sapiensMutation(s): 0 
Gene Names: HLA-A*02:01
Membrane Entity: Yes 
UniProt
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UniProt GroupQ861F7
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinJ [auth M]100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Membrane Entity: Yes 
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Melanoma-associated antigen 4K [auth P]10Homo sapiensMutation(s): 0 
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Find proteins for P43358 (Homo sapiens)
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PHAROS:  P43358
GTEx:  ENSG00000147381 
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UniProt GroupP43358
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Oligosaccharides

Help

Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth H]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth L],
N [auth T]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
S [auth B]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG
Query on NAG

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O [auth A]
P [auth A]
Q [auth A]
R [auth B]
T [auth G]
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
T [auth G],
U [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary