SMTL ID : 8es7.1

CryoEM structure of PN45545 TCR-CD3 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-2-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain C: F.22, N.38, G.75, T.76, D.77, I.78, Y.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.77

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain C: S.40, T.42, N.74, D.81, E.83 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain G: E.64 Chain H: R.28, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain G: Q.168, N.170 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain H: E.81, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain G: Q.76, N.78, L.86, N.87, F.88, Q.89 No protein-ligand interaction detected (PLIP)

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 15 residues within 4Å: Chain B: K.30, Y.33, L.34, F.40, I.41 Chain E: N.111, A.113, T.114, F.120, A.121, V.124 Chain H: S.277, L.281, Y.282, L.285 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain E Hydrophobic interactions: B:Y.33, B:F.40, B:I.41, E:T.114, E:F.120, E:A.121, E:V.124 Salt bridges: B:K.30, B:K.30 Hydrogen bonds: E:N.111

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 1 residues within 4Å: Chain E: N.92 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain E: N.52, F.64 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain G: D.156, N.204 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.204, G:N.204 NAG.11: 1 residues within 4Å: Chain G: N.215 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain H: A.201, N.203 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saotome, K. et al., Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Nat Commun (2023)

Release Date

2023-05-03

Peptides

T-cell surface glycoprotein CD3 zeta chain: AB
T-cell surface glycoprotein CD3 delta chain: C
T-cell surface glycoprotein CD3 epsilon chain: DF
T-cell surface glycoprotein CD3 gamma chain: E
PN45545 TCR alpha chain: G
PN45545 TCR beta chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

B
Y

C
D

D
F

F
E

E
G

G
A

H
B

Membrane

We predict this structure to be a membrane protein.
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T-cell surface glycoprotein CD3 zeta chain

T-cell surface glycoprotein CD3 delta chain

T-cell surface glycoprotein CD3 epsilon chain

T-cell surface glycoprotein CD3 gamma chain

PN45545 TCR alpha chain

PN45545 TCR beta chain

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