9OJU: Vesicle-fusing ATPase

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 4. Determined by electron microscopy at 2.97 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 7
Atoms: 26,513
Mol. weight: 512.69 kDa
Ligands: ADP, ATP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9OJU contains 180 α-helices and 119 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: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	225-235	11
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	1
α-helix	266-276	11
α-helix	279-282	4
β-strand	283-286	4	1
α-helix	287-290	4
β-strand	294	1	2
α-helix	297-303	7
α-helix	307-316	10
β-strand	323-328	6	1
α-helix	330-332	3
α-helix	336-338	3
α-helix	348-358	11
β-strand	367-373	7	1
α-helix	381-384	4
β-strand	391-394	4	1
α-helix	400-417	18
α-helix	426-432	7
α-helix	438-462	25
α-helix	467-473	7
α-helix	478-486	9
β-strand	494	1	3
α-helix	497-502	6
α-helix	513-529	17
β-strand	536-542	7	3
α-helix	549-560	12
β-strand	564-568	5	3
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-603	7	3
β-strand	612	1	4
β-strand	617	1	4
α-helix	620-629	10
β-strand	639-646	8	3
α-helix	649-654	6
β-strand	664-666	3	3
β-strand	670	1	5
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	5
α-helix	707-717	11
α-helix	726-735	10

Chain B: 32 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	6
α-helix	215-218	4
α-helix	224-235	12
α-helix	242-246	5
α-helix	251-253	3
β-strand	255-259	5	7
α-helix	266-276	11
β-strand	277	1	6
α-helix	281-282	2
β-strand	283-286	4	7
β-strand	294	1	8
α-helix	297-303	7
α-helix	307-316	10
β-strand	323-328	6	7
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	7
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	7
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	9
α-helix	426-432	7
α-helix	438-454	17
α-helix	455-457	3
α-helix	467-469	3
β-strand	475	1	9
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	10
α-helix	549-560	12
β-strand	565-568	4	10
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	10
α-helix	605-609	5
β-strand	612	1	11
β-strand	617	1	11
α-helix	620-629	10
β-strand	639-646	8	10
α-helix	649-654	6
α-helix	658-660	3
β-strand	664-666	3	10
β-strand	670	1	12
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	12
α-helix	707-717	11
α-helix	725-736	12

Chain C: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	13
α-helix	215-218	4
α-helix	224-235	12
α-helix	236-238	3
α-helix	242-248	7
α-helix	250-253	4
β-strand	256-259	4	14
α-helix	266-276	11
β-strand	277	1	13
α-helix	281-282	2
β-strand	283-286	4	14
β-strand	294	1	15
α-helix	298-303	6
α-helix	307-316	10
α-helix	317-319	3
β-strand	323-328	6	14
α-helix	330-332	3
β-strand	335	1	16
α-helix	336-337	2
α-helix	349-358	10
β-strand	367-373	7	14
α-helix	376-378	3
β-strand	379	1	16
α-helix	381-384	4
β-strand	391-394	4	14
α-helix	400-416	17
β-strand	420	1	17
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	18
β-strand	464-465	2	18
β-strand	475	1	17
α-helix	477-486	10
α-helix	496-502	7
α-helix	513-529	17
β-strand	536-542	7	19
α-helix	550-560	11
β-strand	564-568	5	19
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	19
α-helix	605-608	4
β-strand	612	1	20
β-strand	617	1	20
α-helix	620-629	10
β-strand	639-646	8	19
α-helix	649-654	6
β-strand	663-666	4	19
β-strand	670	1	21
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	21
α-helix	707-717	11
α-helix	725-736	12

Chain D: 31 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	22
α-helix	215-217	3
α-helix	224-234	11
α-helix	236-239	4
α-helix	242-248	7
β-strand	256-259	4	23
α-helix	266-276	11
β-strand	277	1	22
α-helix	281-282	2
β-strand	283-286	4	23
α-helix	297-303	7
α-helix	307-316	10
β-strand	323-328	6	23
α-helix	330-332	3
α-helix	344-358	15
β-strand	367-373	7	23
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	23
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	24
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
β-strand	457-458	2	25
β-strand	464-465	2	25
β-strand	475	1	24
α-helix	477-486	10
α-helix	496-502	7
α-helix	513-530	18
β-strand	536-542	7	26
α-helix	549-560	12
β-strand	564-568	5	26
α-helix	570-572	3
α-helix	578-594	17
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	639-646	8	26
α-helix	649-654	6
β-strand	664-666	3	26
β-strand	670-672	3	28
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	28
α-helix	707-718	12
α-helix	722-724	3
α-helix	726-736	11

Chain E: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	29
α-helix	215-218	4
α-helix	224-239	16
α-helix	242-248	7
β-strand	255-259	5	30
α-helix	266-276	11
β-strand	277	1	29
α-helix	281-282	2
β-strand	283-285	3	30
α-helix	297-316	20
α-helix	317-319	3
β-strand	323-328	6	30
α-helix	330-333	4
α-helix	346-358	13
β-strand	367-373	7	30
α-helix	376-378	3
α-helix	381-383	3
β-strand	392	1	30
α-helix	400-416	17
β-strand	420	1	31
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
β-strand	457	1	32
β-strand	465	1	32
β-strand	475	1	31
α-helix	477-486	10
α-helix	493-494	2
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	33
α-helix	549-559	11
β-strand	564-568	5	33
α-helix	580-594	15
β-strand	597-602	6	33
α-helix	605-608	4
β-strand	612	1	34
β-strand	617	1	34
α-helix	620-629	10
β-strand	639-646	8	33
α-helix	649-654	6
β-strand	663-666	4	33
β-strand	670	1	35
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	35
α-helix	707-717	11
α-helix	725-736	12

Chain F: 29 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	224-233	10
α-helix	235-237	3
α-helix	242-248	7
β-strand	255-259	5	36
α-helix	265-276	12
β-strand	279	1	37
β-strand	283-286	4	36
α-helix	297-305	9
α-helix	307-316	10
β-strand	322	1	37
β-strand	323-328	6	36
α-helix	330-333	4
α-helix	345-358	14
β-strand	367-373	7	36
α-helix	376-378	3
α-helix	382-384	3
β-strand	391-394	4	36
α-helix	396-398	3
α-helix	400-416	17
β-strand	420	1	38
α-helix	426-432	7
α-helix	438-453	16
α-helix	469-471	3
β-strand	475	1	38
α-helix	477-482	6
α-helix	483-487	5
α-helix	499-502	4
α-helix	512-530	19
β-strand	536-542	7	39
α-helix	549-560	12
β-strand	564-568	5	39
α-helix	570-572	3
α-helix	578-593	16
β-strand	597-602	6	39
α-helix	605-608	4
β-strand	612	1	40
β-strand	617	1	40
α-helix	620-629	10
β-strand	639-645	7	39
α-helix	649-654	6
β-strand	663-666	4	39
β-strand	670-672	3	41
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	41
α-helix	707-718	12
α-helix	725-736	12

Chain H: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	2
β-strand	7	1	8
β-strand	9	1	15

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)
Synaptosomal-associated protein 25	H	protein	84	Rattus norvegicus	P60881 (AlphaFold model)

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

>9OJU_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 (H), FASTA

>9OJU_2 Synaptosomal-associated protein 25 (chains H)
SMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLER
IEEGMDQINKDMKEAEKNLTDLGK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	10

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
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
9OLJ 3.52 Å, 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 18

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