8ES8 | pdb_00008es8

CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)

PDB DOI: https://doi.org/10.2210/pdb8ES8/pdb
EM Map EMD-28571: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2022-10-13 Released: 2023-05-03
Deposition Author(s): Saotome, K., Franklin, M.C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 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

PubMed: 37100770 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-37532-7
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 242.05 kDa
Atom Count: 11,976
Modeled Residue Count: 1,464
Deposited Residue Count: 2,111
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 zeta chain	A [auth Z], B [auth Y]	173	Homo sapiens	Mutation(s): 0 Gene Names: CD247, CD3Z, T3Z, TCRZ Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens) Explore P20963 Go to UniProtKB: P20963
PHAROS: P20963 GTEx: ENSG00000198821
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20963
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 delta chain	C [auth D]	174	Homo sapiens	Mutation(s): 0 Gene Names: CD3D, T3D Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens) Explore P04234 Go to UniProtKB: P04234
PHAROS: P04234 GTEx: ENSG00000167286
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04234
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth D]	Go to GlyGen: P04234-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 epsilon chain	D [auth F], F [auth E]	211	Homo sapiens	Mutation(s): 0 Gene Names: CD3E, T3E Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens) Explore P07766 Go to UniProtKB: P07766
PHAROS: P07766 GTEx: ENSG00000198851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07766
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 gamma chain	E [auth G]	185	Homo sapiens	Mutation(s): 0 Gene Names: CD3G, T3G Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens) Explore P09693 Go to UniProtKB: P09693
PHAROS: P09693 GTEx: ENSG00000160654
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09693
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E [auth G]	Go to GlyGen: P09693-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PN45545 TCR alpha chain	G [auth A]	278	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain G [auth A]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PN45545 TCR beta chain	H [auth B]	319	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain H [auth B]
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	I [auth N]	277	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A02:01 Membrane Entity:* Yes
UniProt
Find proteins for Q861F7 (Homo sapiens) Explore Q861F7 Go to UniProtKB: Q861F7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q861F7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	J [auth M]	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma-associated antigen 4	K [auth P]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P43358 (Homo sapiens) Explore P43358 Go to UniProtKB: P43358
PHAROS: P43358 GTEx: ENSG00000147381
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43358
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth C]	3		N-Glycosylation	Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth T], N [auth U], O [auth V], P [auth Q], Q [auth J]	2		N-Glycosylation	Interactions Focus chain M [auth T] Focus chain N [auth U] Focus chain O [auth V] Focus chain P [auth Q] Focus chain Q [auth J] Interactions & Density Focus chain M [auth T] Focus chain N [auth U] Focus chain O [auth V] Focus chain P [auth Q] Focus chain Q [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain R [auth Y] MOL2 format, chain R [auth Y] mmCIF format, chain R [auth Y]	R [auth Y]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain R [auth Y] Interactions & Density Focus chain R [auth Y]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth G] SDF format, chain S [auth G] MOL2 format, chain W [auth B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth G] MOL2 format, chain S [auth G] mmCIF format, chain W [auth B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth G] mmCIF format, chain S [auth G]	S [auth G], T [auth G], U [auth A], V [auth A], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Interactions & Density Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B]