SMTL ID : 9pd8.1

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 21

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-2-4-1-mer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: G.222, I.223, G.224, G.225, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.224, A:G.225, A:L.226, A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:H.413, A:E.445 ADP.4: 17 residues within 4Å: Chain A: R.388 Chain B: G.222, I.223, G.224, L.226, G.266, C.267, G.268, K.269, T.270, L.271, M.375, I.409, H.413, G.441, A.442, E.445 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.224, B:G.224, B:G.266, B:C.267, B:G.268, B:K.269, B:T.270, B:L.271 ADP.6: 21 residues within 4Å: Chain B: D.362, R.388, R.391 Chain C: G.222, I.223, G.224, G.225, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, M.375, I.409, I.412, H.413, A.442, E.445 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.224, C:G.224, C:G.266, C:G.268, C:K.269, C:T.270, C:T.270, C:T.270, C:L.271, C:H.413, C:E.445, B:R.391 Salt bridges: C:K.269, B:R.388, B:R.388 ADP.8: 20 residues within 4Å: Chain C: K.254, R.388, R.391 Chain D: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.224, D:G.224, D:G.266, D:C.267, D:G.268, D:K.269, D:T.270, D:T.270, D:T.270, D:H.413 Salt bridges: C:R.388, C:R.388 ADP.12: 15 residues within 4Å: Chain F: G.222, I.223, G.224, G.225, P.265, G.266, C.267, G.268, K.269, T.270, L.271, G.405, I.409, I.412, G.441 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.222, F:G.224, F:G.266, F:C.267, F:G.268, F:K.269, F:T.270 Salt bridges: F:K.269

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: I.506, M.507, N.508, G.509, I.510, I.511, K.512, W.513, V.517, P.548, H.549, G.551, K.552, T.553, A.554, L.555, S.650, I.710, K.711, L.714 Chain F: K.634 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.508, A:N.508, A:G.509, A:G.509, A:I.511, A:I.511, A:H.549, A:G.551, A:K.552, A:T.553, A:T.553, A:T.553, A:A.554, A:S.650 Salt bridges: A:K.552, A:K.711, A:K.711, A:K.711 ATP.3: 20 residues within 4Å: Chain A: K.634 Chain B: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:M.507, B:N.508, B:G.509, B:I.511, B:I.511, B:H.549, B:S.550, B:G.551, B:K.552, B:T.553, B:T.553, B:T.553, B:A.554 Salt bridges: B:H.549, B:K.552, B:K.711, B:K.711, B:K.711 ATP.5: 21 residues within 4Å: Chain B: K.634 Chain C: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711, L.714 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:M.507, C:N.508, C:G.509, C:I.511, C:I.511, C:W.513, C:H.549, C:S.550, C:G.551, C:K.552, C:T.553, C:T.553, C:T.553, C:A.554, C:D.607 Salt bridges: C:K.552, C:K.552, C:K.711, C:K.711, C:K.711, B:K.634 ATP.7: 20 residues within 4Å: Chain C: K.634 Chain D: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711, L.714 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:M.507, D:N.508, D:G.509, D:I.511, D:I.511, D:H.549, D:G.551, D:T.553, D:T.553, D:A.554 Salt bridges: D:K.552, D:K.711, D:K.711, D:K.711, C:K.634, C:K.634 ATP.9: 22 residues within 4Å: Chain D: D.362, R.388, R.391 Chain E: G.222, I.223, G.224, G.225, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, M.375, N.377, I.409, H.413, G.441, A.442, E.445 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.224, E:G.266, E:C.267, E:G.268, E:K.269, E:T.270, E:T.270, E:T.270, E:L.271, E:N.377, E:H.413, E:E.445, D:R.388 Salt bridges: E:K.269, D:R.388, D:R.388, D:R.391 ATP.10: 21 residues within 4Å: Chain D: K.634 Chain E: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, D.607, I.710, K.711, L.714 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.508, E:N.508, E:I.511, E:I.511, E:H.549, E:S.550, E:G.551, E:K.552, E:T.553, E:T.553, E:A.554, E:D.607 Salt bridges: E:K.552, E:K.552, E:K.711, D:K.634 ATP.11: 21 residues within 4Å: Chain E: K.634 Chain F: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, K.512, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.508, F:N.508, F:G.509, F:I.511, F:I.511, F:W.513, F:H.549, F:G.551, F:K.552, F:T.553, F:T.553, F:A.554 Salt bridges: F:K.552, F:K.711, F:K.711, E:K.634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, K.I. et al., Pre-fusion AAA+ remodeling of target-SNARE protein complexes enables synaptic transmission. Biorxiv (2024)

Release Date

2025-08-06

Peptides

Vesicle-fusing ATPase: ABCDEF
Synaptosomal-associated protein 25,Synaptosomal-associated protein 25,Synaptosomal-associated protein 25,Alpha-soluble NSF attachment protein: GJ
Syntaxin-1A: HI
Alpha-soluble NSF attachment protein isoform X2: KLMN
unknown sequence: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
J

J
I

H
G

I
H

K
K

L
L

M
M

N
N

O
O

Vesicle-fusing ATPase

Synaptosomal-associated protein 25,Synaptosomal-associated protein 25,Synaptosomal-associated protein 25,Alpha-soluble NSF attachment protein

Syntaxin-1A

Alpha-soluble NSF attachment protein isoform X2

unknown sequence

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