9OK5: Vesicle-fusing ATPase

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 16. Determined by electron microscopy at 3.29 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 7
Atoms: 25,891
Mol. weight: 504.75 kDa
Ligands: PO4, MG, ATP, ADP
Released: 6 Aug 2025

Explore 9OK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OK5 contains 173 α-helices and 112 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	218	1	1
β-strand	220	1	1
α-helix	225-233	9
α-helix	242-248	7
β-strand	255-259	5	2
α-helix	267-276	10
β-strand	283-284	2	2
α-helix	298-304	7
α-helix	307-316	10
β-strand	323-326	4	2
α-helix	330-332	3
β-strand	340	1	3
α-helix	349-358	10
β-strand	367-373	7	2
α-helix	381-383	3
β-strand	392-394	3	2
α-helix	400-410	11
α-helix	412-416	5
α-helix	427-432	6
α-helix	438-462	25
α-helix	467-471	5
α-helix	478-486	9
α-helix	496-499	4
α-helix	513-529	17
β-strand	536-539	4	4
β-strand	541-542	2	5
α-helix	549-559	11
β-strand	564-568	5	4
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	4
α-helix	605-609	5
β-strand	612	1	6
β-strand	617	1	6
α-helix	620-629	10
α-helix	633-634	2
β-strand	640-643	4	4
β-strand	646	1	5
α-helix	649-654	6
β-strand	665-666	2	5
β-strand	670	1	7
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	7
α-helix	707-717	11
α-helix	725-735	11

Chain B: 31 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	8
α-helix	215-218	4
α-helix	225-235	11
α-helix	236-238	3
α-helix	242-248	7
β-strand	256-259	4	9
α-helix	266-276	11
β-strand	277	1	8
α-helix	280-282	3
β-strand	283-285	3	9
β-strand	294	1	10
α-helix	298-303	6
α-helix	304-306	3
α-helix	307-315	9
α-helix	320-322	3
β-strand	323-328	6	9
α-helix	345-347	3
α-helix	349-358	10
β-strand	367-373	7	9
α-helix	381-383	3
β-strand	391-394	4	9
α-helix	400-416	17
β-strand	420	1	11
α-helix	426-432	7
α-helix	438-455	18
α-helix	467-471	5
β-strand	475	1	11
α-helix	477-483	7
α-helix	499-502	4
α-helix	512-530	19
β-strand	536-542	7	12
α-helix	549-558	10
β-strand	565-568	4	12
α-helix	570-572	3
β-strand	576	1	3
α-helix	578-592	15
β-strand	599-602	4	12
α-helix	605-608	4
β-strand	612	1	13
β-strand	617	1	13
α-helix	620-629	10
α-helix	633-634	2
β-strand	640-646	7	12
α-helix	649-654	6
β-strand	664-666	3	12
β-strand	670	1	14
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	14
α-helix	707-717	11
α-helix	725-735	11

Chain C: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	15
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	16
α-helix	267-276	10
β-strand	277	1	15
β-strand	283-285	3	16
β-strand	294	1	17
α-helix	298-303	6
α-helix	307-316	10
β-strand	323-328	6	16
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-372	6	16
α-helix	381-383	3
β-strand	391-394	4	16
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	18
α-helix	426-432	7
α-helix	438-456	19
α-helix	469-471	3
β-strand	475	1	18
α-helix	477-482	6
α-helix	483-487	5
α-helix	498-502	5
α-helix	513-529	17
β-strand	536-542	7	19
α-helix	550-558	9
β-strand	564-568	5	19
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	19
α-helix	605-608	4
β-strand	612	1	20
β-strand	617	1	20
α-helix	620-629	10
α-helix	632-634	3
β-strand	640-646	7	19
α-helix	649-654	6
β-strand	665-666	2	19
β-strand	670	1	21
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	21
α-helix	707-716	10
α-helix	725-736	12

Chain D: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	22
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-245	4
α-helix	251-253	3
β-strand	256-259	4	23
α-helix	267-276	10
β-strand	277	1	22
α-helix	281-282	2
β-strand	283-285	3	23
β-strand	294	1	24
α-helix	297-302	6
α-helix	307-315	9
β-strand	323-328	6	23
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	23
α-helix	381-383	3
β-strand	391-392	2	23
α-helix	400-410	11
α-helix	415-417	3
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	25
β-strand	464-465	2	25
α-helix	469-472	4
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	26
α-helix	549-558	10
β-strand	564-568	5	26
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	26
α-helix	605-608	4
β-strand	612	1	27
β-strand	617	1	27
α-helix	620-629	10
β-strand	639-645	7	26
α-helix	649-654	6
β-strand	665-666	2	26
β-strand	670	1	28
α-helix	673-683	11
α-helix	688-696	9
β-strand	705	1	28
α-helix	708-717	10
α-helix	725-735	11

Chain E: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	225-233	9
α-helix	242-248	7
β-strand	256-259	4	29
α-helix	266-273	8
α-helix	281-282	2
β-strand	283-286	4	29
α-helix	297-303	7
α-helix	307-315	9
β-strand	323-328	6	29
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	29
α-helix	376-378	3
α-helix	381-384	4
β-strand	391-394	4	29
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	30
α-helix	426-432	7
α-helix	438-455	18
β-strand	457	1	31
β-strand	465	1	31
β-strand	475	1	30
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	32
α-helix	550-559	10
β-strand	566-568	3	32
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	32
α-helix	605-607	3
β-strand	612	1	33
β-strand	617	1	33
α-helix	620-629	10
β-strand	640-646	7	32
α-helix	649-654	6
β-strand	663-666	4	32
α-helix	673-683	11
α-helix	689-698	10
α-helix	707-717	11
α-helix	725-737	13

Chain F: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	226-238	13
α-helix	242-248	7
α-helix	250-253	4
β-strand	256-259	4	34
α-helix	266-276	11
α-helix	280-282	3
β-strand	283-285	3	34
α-helix	288-290	3
α-helix	297-316	20
β-strand	325-328	4	34
α-helix	330-333	4
α-helix	346-359	14
β-strand	370-373	4	34
α-helix	382-384	3
β-strand	391-394	4	34
α-helix	400-415	16
β-strand	420	1	35
α-helix	426-432	7
α-helix	438-458	21
α-helix	468-471	4
β-strand	475	1	35
α-helix	477-486	10
α-helix	495-502	8
α-helix	513-529	17
β-strand	536-542	7	36
α-helix	550-559	10
β-strand	564-568	5	36
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-603	7	36
α-helix	605-608	4
β-strand	612	1	37
β-strand	617	1	37
α-helix	620-629	10
β-strand	639-646	8	36
α-helix	649-654	6
β-strand	665-666	2	36
α-helix	668-669	2
β-strand	670	1	38
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	38
α-helix	707-718	12
α-helix	726-735	10

Chain G: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	10
β-strand	10	1	17
β-strand	12	1	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vesicle-fusing ATPase	A, B, C, D, E, F	protein	747	Cricetulus griseus	P18708 (AlphaFold model)
Undefined N-terminus of SNAP-25 or syntaxin-1a	G	protein	14	Rattus norvegicus

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9OK5_1 Vesicle-fusing ATPase (chains A, B, C, D, E, F)
GAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVP
GSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKM
AAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLV
VGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFAS
RVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGE
SEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSK
IDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGH
QLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTR
GDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLV
SVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQL
SCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEM
LNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS
LQMDPEYRVRKFLALLREEGASPLDFD

Sequence of entity 2 (G), FASTA

>9OK5_2 Undefined N-terminus of SNAP-25 or syntaxin-1a (chains G)
XXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
MG	Magnesium ion	Mg	9
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	7
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

Primary citation

Structural remodeling of target-SNARE protein complexes by NSF enables synaptic transmission. White, K.I., Khan, Y.A., Qiu, K. et al. Nat Commun (2025) 16:8371-8371. DOI 10.1038/s41467-025-62764-0 · PubMed

Other PDB entries of the same protein (UniProt P18708 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1D2N 1.75 Å, D2 domain of N-ethylmaleimide-sensitive fusion protein
1NSF 1.9 Å, D2 hexamerization domain of N-ethylmaleimide sensitive factor (NSF)
1QCS 1.9 Å, N-terminal domain of N-ethylmaleimide sensitive factor (NSF)
1QDN 2.3 Å, Amino terminal domain of the N-ethylmaleimide sensitive fusion protein (NSF)
9OJR 2.95 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 3
9OJU 2.97 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 4
9PFF 3.09 Å, Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), non-hydrolyzing,…
9PFC 3.15 Å, NSF, substrate free, hydrolyzing, class 26
9OJZ 3.39 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5
9PB9 3.45 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 8
9PBA 3.47 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 9
9OLJ 3.52 Å, 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 18

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