› 8es8

Electron Microscopy
2.65Å resolution

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

Released:
DOI: 10.2210/pdb8es8/pdb
PDB entry 8es8 coloured by chain, front view.
PDB entry 8es8 coloured by chain, side view.
PDB entry 8es8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM.
Saotome K, Dudgeon D, Colotti K, Moore MJ, Jones J, Zhou Y, Rafique A, Yancopoulos GD, Murphy AJ, Lin JC, Olson WC, Franklin MC
Nat Commun 14 2401 (2023)
PMID: 37100770
Related structures: EMD-28571

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-225026 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (11 distinct):
T-cell surface glycoprotein CD3 zeta chain Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 173 amino acids
Theoretical weight: 19.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P20963 (Residues: 1-164; Coverage: 100%)
Gene names: CD247, CD3Z, T3Z, TCRZ
Sequence domains:
T-cell surface glycoprotein CD3 delta chain Chain: D
Molecule details ›
Chain: D
Length: 174 amino acids
Theoretical weight: 19.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P04234 (Residues: 1-171; Coverage: 100%)
Gene names: CD3D, T3D
Sequence domains:
T-cell surface glycoprotein CD3 epsilon chain Chains: E, F
Molecule details ›
Chains: E, F
Length: 211 amino acids
Theoretical weight: 23.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P07766 (Residues: 2-207; Coverage: 100%)
Gene names: CD3E, T3E
Sequence domains:
T-cell surface glycoprotein CD3 gamma chain Chain: G
Molecule details ›
Chain: G
Length: 185 amino acids
Theoretical weight: 20.69 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P09693 (Residues: 1-182; Coverage: 100%)
Gene names: CD3G, T3G
Sequence domains:
PN45545 TCR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 278 amino acids
Theoretical weight: 30.74 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
PN45545 TCR beta chain Chain: B
Molecule details ›
Chain: B
Length: 319 amino acids
Theoretical weight: 35.89 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Ig-like domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 277 amino acids
Theoretical weight: 32.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q861F7 (Residues: 1-276; Coverage: 81%)
Gene name: HLA-A
Sequence domains:
Beta-2-microglobulin Chain: M
Molecule details ›
Chain: M
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Melanoma-associated antigen 4 Chain: P
Molecule details ›
Chain: P
Length: 10 amino acids
Theoretical weight: 1.13 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P43358 (Residues: 230-239; Coverage: 3%)
Gene names: MAGE4, MAGEA4

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand Y01 1 x Y01
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.65Å
Relevant EMDB volumes: EMD-28571
Expression systems:
  • Homo sapiens
  • Escherichia coli
  • Not provided

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