SMTL ID : 9c3e.1

TCR - CD3 complex bound to HLA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-1-2-1-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, K.23, N.38, T.76, D.77, I.78, Y.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.79

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.2: 3 residues within 4Å: Chain A: I.26, N.41, R.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.91 NAG.3: 2 residues within 4Å: Chain A: T.77, N.82 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.77 Hydrogen bonds: A:T.77 NAG.4: 3 residues within 4Å: Chain A: Q.164, T.165, N.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.164 NAG.5: 3 residues within 4Å: Chain A: D.152, K.153, N.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.153, A:N.200 NAG.6: 1 residues within 4Å: Chain A: N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.7: 3 residues within 4Å: Chain B: N.84, S.86, R.96 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.86, B:R.96 NAG.8: 4 residues within 4Å: Chain C: S.40, N.74, D.81, E.83 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain F: K.51, N.52, F.64 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL

CLR.10: 13 residues within 4Å: Chain A: N.264, L.265, T.268 Chain B: L.284, K.287, Y.291 Chain F: S.125, V.128, G.132, F.135 Chain H: F.40, V.44, T.47 9 PLIP interactions: 2 interactions with chain H, 4 interactions with chain B, 2 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: H:F.40, H:V.44, B:L.284, B:L.284, B:K.287, B:Y.291, A:L.265, A:T.268, F:F.135 CLR.11: 10 residues within 4Å: Chain B: S.276, L.284 Chain F: F.120, V.124 Chain H: K.30, Y.33, L.34, D.36, G.37, F.40 7 PLIP interactions: 4 interactions with chain H, 1 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: H:K.30, H:Y.33, H:L.34, H:F.40, F:F.120, F:V.124 Hydrogen bonds: B:S.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Notti, R.Q. et al., The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex. Biorxiv (2024)

Release Date

2024-10-02

Peptides

TCRa: A
TCRb (EGFP fusion): B
T-cell surface glycoprotein CD3 delta chain: C
T-cell surface glycoprotein CD3 epsilon chain: DE
T-cell surface glycoprotein CD3 gamma chain: F
T-cell surface glycoprotein CD3 zeta chain: GH
Cancer/testis antigen 1,Beta-2-microglobulin,MHC class I antigen: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

G
X

H
Y

I
H

Membrane

We predict this structure to be a membrane protein.
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TCRa

TCRb (EGFP fusion)

T-cell surface glycoprotein CD3 delta chain

T-cell surface glycoprotein CD3 epsilon chain

T-cell surface glycoprotein CD3 gamma chain

T-cell surface glycoprotein CD3 zeta chain

Cancer/testis antigen 1,Beta-2-microglobulin,MHC class I antigen

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