SMTL ID : 8tw4.1

TCR in nanodisc ND-I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: T.77, R.80, L.81, N.82, Y.95 Chain E: D.77 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: Q.33 Chain E: N.74, E.83, T.85 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain F: K.51, N.52, F.64 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: N.211, N.212, S.213, I.214 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.214 Hydrogen bonds: A:N.211, A:N.211, A:N.211, A:N.211 NAG.5: 4 residues within 4Å: Chain A: L.30, V.39, L.40, N.41 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.30 Hydrogen bonds: A:V.39, A:V.39, A:N.41 NAG.7: 3 residues within 4Å: Chain F: N.28, N.92, K.93 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.28

2 x CLR: CHOLESTEROL

CLR.6: 10 residues within 4Å: Chain A: L.257, V.260, A.261, L.265 Chain B: L.284 Chain F: F.120, A.121, V.124 Chain H: V.44 Ligands: CLR.8 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain F, 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: A:L.257, A:V.260, A:A.261, A:L.265, A:L.265, F:F.120, F:F.120, F:A.121, F:V.124, F:V.124, B:L.284, H:V.44 CLR.8: 6 residues within 4Å: Chain B: A.277 Chain F: A.113, F.120 Chain H: Y.33, D.36 Ligands: CLR.6 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: B:A.277, F:A.113, F:F.120, H:D.36

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

TCR alpha: A
T cell receptor beta variable 6-5, T cell receptor beta chain MC.7.G5, MCHERRY fusion protein: B
T-cell surface glycoprotein CD3 epsilon chain: CD
T-cell surface glycoprotein CD3 delta chain: E
T-cell surface glycoprotein CD3 gamma chain: F
T-cell surface glycoprotein CD3 zeta chain,RNA-directed RNA polymerase L: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
D

F
G

G
X

H
Y

Membrane

We predict this structure to be a membrane protein.
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TCR alpha

T cell receptor beta variable 6-5, T cell receptor beta chain MC.7.G5, MCHERRY fusion protein

T-cell surface glycoprotein CD3 epsilon chain

T-cell surface glycoprotein CD3 delta chain

T-cell surface glycoprotein CD3 gamma chain

T-cell surface glycoprotein CD3 zeta chain,RNA-directed RNA polymerase L

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