SMTL ID : 9jqr.1

Cryo-EM structure of the Vgamma9Vdelta2 TCR-engaged BTN3A1-BTN3A2-BTN2A1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 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: 4 residues within 4Å: Chain C: N.134 Chain F: P.134, T.135, I.136 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain D: P.10, N.92, G.93, L.112, V.113, Y.143 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.10

1 x H6P: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate(Non-covalent)

H6P.3: 13 residues within 4Å: Chain A: W.351, H.352, Y.353, W.392, M.395, R.413, R.419, R.470, L.472 Chain D: G.480, V.481, V.483 Chain E: R.449 10 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: A:W.351, A:L.472, A:L.472 Hydrogen bonds: A:H.352, A:Y.353, D:V.483 Salt bridges: A:R.413, A:R.419, A:R.470, E:R.449

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

NAG.4: 1 residues within 4Å: Chain B: N.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.86 NAG.5: 2 residues within 4Å: Chain D: N.18, H.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.18, D:H.85 NAG.6: 1 residues within 4Å: Chain D: N.86 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain D: N.194, T.196, G.199 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.194 NAG.8: 2 residues within 4Å: Chain E: N.18, H.85 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.18 NAG.9: 1 residues within 4Å: Chain E: N.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.86 NAG.10: 5 residues within 4Å: Chain E: N.92, G.93, L.112, V.113, Y.143 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.93, E:Y.143 NAG.11: 2 residues within 4Å: Chain E: P.153, N.188 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.153 NAG.12: 4 residues within 4Å: Chain E: N.194, T.196, G.199, K.201 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Structures of butyrophilin multimers reveal a plier-like mechanism for V gamma 9V delta 2 T cell receptor activation. Immunity (2025)

Release Date

2025-06-18

Peptides

Butyrophilin subfamily 3 member A1: A
Butyrophilin subfamily 3 member A2: B
Vdelta2 T cell receptor: C
Butyrophilin subfamily 2 member A1: DE
Vgamma9 T cell receptor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

Membrane

We predict this structure to be a membrane protein.
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Butyrophilin subfamily 3 member A1

Butyrophilin subfamily 3 member A2

Vdelta2 T cell receptor

Butyrophilin subfamily 2 member A1

Vgamma9 T cell receptor

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