SMTL ID : 6mdn.1

The 20S supercomplex engaging the SNAP-25 N-terminus (class 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, D.628, S.671, I.731, K.732, L.735 Chain F: K.655 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:N.529, A:N.529, A:I.532, A:H.570, A:S.571, A:G.572, A:T.574 Salt bridges: A:H.570, A:K.573, A:K.732, F:K.655, F:K.655, F:K.655 ATP.3: 23 residues within 4Å: Chain A: L.379, D.383, R.409, R.412 Chain B: I.244, G.245, L.247, P.285, P.286, G.287, C.288, G.289, K.290, T.291, L.292, E.353, N.398, I.430, I.433, H.434, G.462, A.463, E.466 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.245, B:G.245, B:P.286, B:G.289, B:K.290, B:T.291, B:L.292, B:H.434, A:R.409, A:R.412 Salt bridges: B:K.290, B:K.290, A:R.409, A:R.409, A:R.412, A:R.412 ATP.4: 22 residues within 4Å: Chain A: K.655 Chain B: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, I.731, K.732, L.735 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.529, B:G.530, B:I.532, B:I.532, B:S.571, B:G.572, B:K.573, B:T.574, B:T.574, B:A.575 Salt bridges: B:K.573, B:K.573, B:K.732, B:K.732, B:K.732, A:K.655, A:K.655 ATP.5: 22 residues within 4Å: Chain B: K.655 Chain C: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.529, C:N.529, C:I.532, C:I.532, C:H.570, C:S.571, C:S.571, C:G.572, C:K.573, C:T.574, C:T.574 Salt bridges: C:K.573, C:K.573, C:K.732, C:K.732, C:K.732, B:K.655 ATP.6: 24 residues within 4Å: Chain B: K.275, D.383, R.409, R.412 Chain C: G.243, I.244, G.245, L.247, P.285, P.286, G.287, C.288, G.289, K.290, T.291, L.292, E.353, N.398, I.430, H.434, S.461, G.462, A.463, E.466 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:G.245, C:G.245, C:G.287, C:C.288, C:G.289, C:K.290, C:T.291, C:L.292, C:N.398, C:N.398 Salt bridges: C:K.290, B:R.409, B:R.409, B:R.409, B:R.412, B:R.412 ATP.7: 24 residues within 4Å: Chain C: K.655 Chain D: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732, L.735 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:M.528, D:N.529, D:N.529, D:N.529, D:I.532, D:I.532, D:W.534, D:H.570, D:S.571, D:G.572, D:K.573 Salt bridges: D:H.570, D:K.573, D:K.732, D:K.732, C:K.655 ATP.8: 22 residues within 4Å: Chain C: K.275, D.383, R.409, R.412 Chain D: G.243, I.244, G.246, P.286, G.287, C.288, G.289, K.290, T.291, L.292, R.295, N.398, I.430, I.433, H.434, G.462, A.463, E.466 18 PLIP interactions: 6 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:K.275, D:G.287, D:C.288, D:G.289, D:K.290, D:T.291, D:L.292, D:R.295, D:N.398, D:N.398, D:A.463 Salt bridges: C:R.409, C:R.409, C:R.409, C:R.412, C:R.412, D:K.290, D:K.290 ATP.9: 23 residues within 4Å: Chain D: K.655 Chain E: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732, L.735 19 PLIP interactions: 17 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:M.528, E:N.529, E:N.529, E:I.532, E:W.534, E:H.570, E:G.572, E:K.573, E:T.574, E:T.574, E:A.575, E:D.628 Salt bridges: E:K.573, E:K.573, E:K.732, E:K.732, E:K.732, D:K.655, D:K.655 ATP.11: 22 residues within 4Å: Chain E: K.655 Chain F: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, D.628, S.671, I.731, K.732, L.735 22 PLIP interactions: 20 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.529, F:N.529, F:N.529, F:I.532, F:I.532, F:W.534, F:H.570, F:S.571, F:S.571, F:G.572, F:K.573, F:T.574, F:T.574, F:T.574, F:A.575 Salt bridges: F:K.573, F:K.573, F:K.732, F:K.732, F:K.732, E:K.655, E:K.655

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

ADP.2: 16 residues within 4Å: Chain A: G.243, I.244, G.245, L.247, P.286, G.287, C.288, G.289, K.290, T.291, L.292, I.430, H.434, G.462, A.463, E.466 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.245, A:G.245, A:P.286, A:P.286, A:C.288, A:G.289, A:T.291, A:T.291 Salt bridges: A:K.290 ADP.10: 20 residues within 4Å: Chain D: K.275, R.409, R.412 Chain E: I.244, G.245, G.246, P.286, G.287, C.288, G.289, K.290, T.291, L.292, N.398, I.430, I.433, H.434, G.462, A.463, E.466 14 PLIP interactions: 5 interactions with chain D, 9 interactions with chain E Hydrogen bonds: D:R.409, D:R.412, E:I.244, E:C.288, E:G.289, E:K.290, E:T.291, E:T.291, E:N.398, E:N.398 Salt bridges: D:R.409, D:R.409, D:R.412, E:K.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, K.I. et al., Structural principles of SNARE complex recognition by the AAA+ protein NSF. Elife (2018)

Release Date

2018-09-19

Peptides

Vesicle-fusing ATPase: ABCDEF
Synaptosomal-associated protein 25: G
Syntaxin-1A: H
Vesicle-associated membrane protein 2: I
Alpha-soluble NSF attachment protein: JK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

Vesicle-fusing ATPase

Synaptosomal-associated protein 25

Syntaxin-1A

Vesicle-associated membrane protein 2

Alpha-soluble NSF attachment protein

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