9OKC: Vesicle-fusing ATPase

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 17. Determined by electron microscopy at 3.67 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.67 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 7
Atoms: 25,045
Mol. weight: 504.58 kDa
Ligands: MG, PO4, ATP, ADP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9OKC contains 170 α-helices and 103 β-strands across 6 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: 29 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	224-233	10
α-helix	235-238	4
α-helix	242-248	7
β-strand	255-256	2	1
β-strand	259	1	2
α-helix	266-276	11
β-strand	284-285	2	3
α-helix	287-289	3
α-helix	299-316	18
α-helix	320-322	3
β-strand	326-327	2	3
α-helix	330-332	3
α-helix	350-358	9
β-strand	369-370	2	1
β-strand	373	1	2
α-helix	376-378	3
α-helix	381-384	4
β-strand	394	1	2
α-helix	400-407	8
α-helix	412-416	5
α-helix	426-432	7
α-helix	438-462	25
α-helix	469-473	5
α-helix	479-486	8
α-helix	497-502	6
α-helix	512-529	18
β-strand	536-538	3	4
β-strand	541-542	2	5
α-helix	550-558	9
β-strand	564-568	5	4
α-helix	570-572	3
α-helix	578-594	17
β-strand	598-602	5	4
β-strand	612	1	6
β-strand	617	1	6
α-helix	620-629	10
α-helix	632-634	3
β-strand	640-643	4	4
β-strand	645-646	2	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	726-735	10

Chain B: 29 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	215-217	3
α-helix	225-233	9
α-helix	236-239	4
α-helix	242-248	7
α-helix	250-253	4
β-strand	256-259	4	8
α-helix	266-276	11
β-strand	283	1	9
α-helix	298-316	19
β-strand	325	1	9
β-strand	335	1	10
α-helix	336-337	2
α-helix	347-358	12
β-strand	369	1	9
β-strand	370-373	4	8
α-helix	376-378	3
β-strand	379	1	10
β-strand	386	1	11
β-strand	388	1	11
β-strand	392-394	3	8
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	12
α-helix	426-432	7
α-helix	438-454	17
α-helix	455-457	3
β-strand	475	1	12
α-helix	477-482	6
α-helix	483-487	5
α-helix	497-502	6
α-helix	512-530	19
β-strand	536-539	4	13
β-strand	540-542	3	14
α-helix	550-560	11
β-strand	566-568	3	13
α-helix	571-573	3
α-helix	578-590	13
β-strand	600-602	3	13
α-helix	605-608	4
α-helix	620-629	10
β-strand	640-643	4	13
α-helix	649-654	6
β-strand	664-666	3	14
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-717	11
α-helix	726-736	11

Chain C: 31 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	15
α-helix	224-230	7
α-helix	231-235	5
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	16
α-helix	266-276	11
β-strand	277	1	15
α-helix	280-282	3
α-helix	298-316	19
β-strand	325-328	4	16
α-helix	330-332	3
α-helix	335-337	3
α-helix	349-358	10
β-strand	369-373	5	16
α-helix	381-383	3
β-strand	391-394	4	16
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-455	18
α-helix	470-472	3
α-helix	477-482	6
α-helix	483-487	5
α-helix	498-502	5
α-helix	513-530	18
β-strand	536-542	7	17
α-helix	550-560	11
β-strand	564-568	5	17
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	17
α-helix	605-609	5
β-strand	612	1	18
β-strand	617	1	18
α-helix	620-627	8
α-helix	628-630	3
β-strand	639-645	7	17
α-helix	649-654	6
β-strand	663-666	4	17
α-helix	668-669	2
β-strand	670	1	19
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	19
α-helix	707-717	11
α-helix	725-736	12

Chain D: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	225-234	10
α-helix	236-238	3
α-helix	242-247	6
β-strand	256-259	4	20
α-helix	266-275	10
β-strand	283-284	2	20
α-helix	297-316	20
β-strand	323-328	6	20
α-helix	346-358	13
β-strand	367-372	6	20
α-helix	381-384	4
β-strand	391-394	4	20
α-helix	400-410	11
α-helix	412-416	5
α-helix	426-432	7
α-helix	438-454	17
α-helix	470-472	3
α-helix	477-486	10
α-helix	496-499	4
α-helix	513-529	17
β-strand	538-542	5	21
α-helix	549-558	10
β-strand	564-567	4	21
α-helix	578-593	16
β-strand	597	1	22
β-strand	598-602	5	21
α-helix	605-609	5
β-strand	612	1	23
β-strand	617	1	23
α-helix	620-629	10
β-strand	639	1	22
β-strand	642-646	5	21
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	21
β-strand	670	1	24
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	24
α-helix	708-718	11
α-helix	725-736	12

Chain E: 27 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	25
α-helix	225-234	10
α-helix	236-239	4
α-helix	242-248	7
β-strand	255-258	4	26
β-strand	259	1	27
α-helix	266-276	11
β-strand	277	1	25
α-helix	281-282	2
β-strand	283-284	2	26
α-helix	299-313	15
α-helix	317-319	3
β-strand	323-328	6	26
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-372	6	26
α-helix	381-383	3
β-strand	389-391	3	26
β-strand	394	1	27
α-helix	400-416	17
β-strand	420	1	28
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
α-helix	469-472	4
β-strand	475	1	28
α-helix	477-482	6
α-helix	483-487	5
α-helix	512-529	18
β-strand	538-542	5	29
α-helix	549-558	10
β-strand	564-568	5	29
α-helix	578-593	16
β-strand	597	1	30
β-strand	598-602	5	29
α-helix	605-608	4
β-strand	612	1	31
β-strand	617	1	31
α-helix	620-631	12
β-strand	639	1	30
β-strand	642-646	5	29
α-helix	649-654	6
β-strand	663-666	4	29
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-718	12
α-helix	725-736	12

Chain F: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	225-234	10
α-helix	236-239	4
α-helix	242-248	7
β-strand	256-259	4	32
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-286	4	32
α-helix	297-304	8
α-helix	307-316	10
β-strand	323-328	6	32
α-helix	330-333	4
α-helix	345-358	14
β-strand	367-372	6	32
α-helix	381-383	3
β-strand	391-394	4	32
α-helix	396-398	3
α-helix	400-409	10
α-helix	412-417	6
α-helix	426-432	7
α-helix	438-454	17
α-helix	477-486	10
α-helix	512-529	18
β-strand	538-542	5	33
α-helix	550-560	11
β-strand	564-568	5	33
α-helix	570-572	3
α-helix	578-594	17
β-strand	597	1	34
β-strand	598-602	5	33
α-helix	605-608	4
β-strand	612	1	35
β-strand	617	1	35
α-helix	621-629	9
α-helix	633-634	2
β-strand	639	1	34
β-strand	642-645	4	33
α-helix	649-654	6
β-strand	663-666	4	33
β-strand	670-672	3	36
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	36
α-helix	707-717	11
α-helix	725-736	12

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	12	Rattus norvegicus

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

>9OKC_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

>9OKC_2 Undefined N-terminus of SNAP-25 or syntaxin-1a (chains G)
XXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
PO4	Phosphate ion	O4 P	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4

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
9OK5 3.29 Å, 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 16
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

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