9PBV: Vesicle-fusing ATPase

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 11. Determined by electron microscopy at 3.91 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.91 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 12
Atoms: 37,430
Mol. weight: 689.94 kDa
Ligands: ADP, ATP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PBV contains 236 α-helices and 140 β-strands across 12 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	225-235	11
α-helix	236-238	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	1
α-helix	267-275	9
β-strand	283-286	4	1
α-helix	287-290	4
β-strand	294	1	2
α-helix	298-303	6
α-helix	307-316	10
β-strand	325-328	4	1
α-helix	330-332	3
α-helix	348-358	11
β-strand	369-373	5	1
α-helix	381-384	4
β-strand	392-394	3	1
α-helix	400-417	18
α-helix	426-432	7
α-helix	438-460	23
α-helix	467-471	5
α-helix	472-475	4
α-helix	477-484	8
α-helix	499-502	4
α-helix	513-529	17
β-strand	536-542	7	3
α-helix	549-560	12
β-strand	567-568	2	3
α-helix	570-573	4
α-helix	578-593	16
β-strand	600-602	3	3
β-strand	612	1	4
β-strand	617	1	4
α-helix	620-629	10
α-helix	632-634	3
β-strand	640-645	6	3
α-helix	649-654	6
β-strand	664-666	3	3
α-helix	673-683	11
α-helix	688-697	10
α-helix	707-718	12
α-helix	726-735	10

Chain B: 35 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	5
α-helix	14-19	6
β-strand	22	1	6
β-strand	23-24	2	5
β-strand	34-40	7	5
β-strand	43-48	6	5
β-strand	49	1	6
α-helix	56	1
β-strand	59-62	4	5
α-helix	64-70	7
β-strand	77-83	7	5
α-helix	87-90	4
β-strand	91	1	7
β-strand	94-100	7	8
β-strand	111-113	3	9
α-helix	114-125	12
β-strand	129-131	3	7
β-strand	135-140	6	8
β-strand	143-152	10	8
β-strand	174-176	3	7
β-strand	182-187	6	8
β-strand	194-196	3	9
β-strand	209	1	10
α-helix	215-218	4
α-helix	224-235	12
α-helix	236-238	3
α-helix	242-248	7
β-strand	255-259	5	11
α-helix	267-276	10
β-strand	277	1	10
α-helix	281-282	2
β-strand	283-285	3	11
β-strand	294	1	12
α-helix	297-316	20
β-strand	325-327	3	11
α-helix	330-332	3
α-helix	347-358	12
β-strand	369-373	5	11
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	11
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	13
α-helix	426-432	7
α-helix	439-455	17
β-strand	475	1	13
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-530	19
β-strand	538-542	5	14
α-helix	549-560	12
β-strand	565-568	4	14
α-helix	570-572	3
α-helix	578-593	16
β-strand	599-602	4	14
α-helix	605-609	5
β-strand	612	1	15
β-strand	617	1	15
α-helix	620-629	10
β-strand	642-646	5	14
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	14
β-strand	670	1	16
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	16
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-736	12

Chain C: 31 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	28
α-helix	216-218	3
α-helix	224-234	11
α-helix	236-238	3
α-helix	242-248	7
β-strand	256-259	4	29
α-helix	266-275	10
β-strand	277	1	28
α-helix	281-282	2
β-strand	285-286	2	29
α-helix	297-316	20
α-helix	317-319	3
β-strand	327-328	2	29
α-helix	330-333	4
β-strand	335	1	30
α-helix	336-337	2
α-helix	349-358	10
β-strand	370-373	4	29
β-strand	379	1	30
α-helix	381-384	4
β-strand	391-394	4	29
α-helix	400-412	13
α-helix	413-417	5
α-helix	426-432	7
α-helix	438-454	17
β-strand	458	1	31
β-strand	464	1	31
α-helix	470-472	3
α-helix	477-485	9
α-helix	496-502	7
α-helix	513-529	17
β-strand	536-542	7	32
α-helix	550-559	10
β-strand	566-568	3	32
α-helix	570-572	3
α-helix	578-591	14
β-strand	600-602	3	32
α-helix	605-608	4
β-strand	612	1	33
β-strand	617	1	33
α-helix	620-629	10
α-helix	633-634	2
β-strand	640-645	6	32
α-helix	649-654	6
β-strand	665-666	2	32
β-strand	670	1	34
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	34
α-helix	707-718	12
α-helix	725-736	12

Chain D: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	35
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	36
α-helix	266-276	11
β-strand	277	1	35
α-helix	281-282	2
β-strand	283-285	3	36
α-helix	298-305	8
α-helix	307-316	10
β-strand	323-328	6	36
α-helix	348-358	11
β-strand	367-373	7	36
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	36
α-helix	400-409	10
β-strand	420	1	37
α-helix	426-432	7
α-helix	438-454	17
β-strand	475	1	37
α-helix	477-486	10
α-helix	496-502	7
α-helix	513-530	18
β-strand	536-542	7	38
α-helix	549-560	12
β-strand	564-568	5	38
α-helix	570-572	3
α-helix	578-594	17
β-strand	597-603	7	38
α-helix	605-608	4
α-helix	620-629	10
β-strand	639-646	8	38
α-helix	649-654	6
α-helix	658-660	3
β-strand	664-666	3	38
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-718	12
α-helix	722-724	3
α-helix	725-736	12

Chain E: 32 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	17
α-helix	14-18	5
β-strand	22-24	3	17
β-strand	34-40	7	17
β-strand	43-51	9	17
α-helix	56	1
β-strand	59-62	4	17
α-helix	64-69	6
β-strand	77-82	6	17
α-helix	87-90	4
β-strand	91	1	18
β-strand	94-101	8	19
α-helix	104-106	3
β-strand	112-113	2	20
α-helix	114-124	11
β-strand	129-131	3	18
β-strand	135-140	6	19
β-strand	143-152	10	19
β-strand	174-176	3	18
β-strand	182-187	6	19
β-strand	195-196	2	20
β-strand	209	1	21
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-248	7
β-strand	255-259	5	22
α-helix	266-276	11
β-strand	277	1	21
α-helix	281-282	2
β-strand	283-285	3	22
α-helix	297-316	20
α-helix	317-319	3
β-strand	323-328	6	22
α-helix	330-332	3
α-helix	348-358	11
β-strand	359	1	23
β-strand	363	1	23
β-strand	367-373	7	22
α-helix	376-378	3
β-strand	392	1	22
α-helix	400-416	17
β-strand	420	1	24
α-helix	426-432	7
α-helix	438-456	19
β-strand	475	1	24
α-helix	477-486	10
α-helix	499-502	4
α-helix	512-529	18
β-strand	538-542	5	25
α-helix	549-559	11
β-strand	564-568	5	25
α-helix	580-591	12
β-strand	598-602	5	25
α-helix	606-608	3
β-strand	612	1	26
β-strand	617	1	26
α-helix	620-629	10
β-strand	642-646	5	25
α-helix	649-654	6
β-strand	664-666	3	25
β-strand	670	1	27
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	27
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-736	12

Chain F: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	224-230	7
α-helix	231-235	5
α-helix	242-248	7
β-strand	255-259	5	39
α-helix	265-276	12
β-strand	279	1	40
β-strand	283	1	39
α-helix	297-316	20
β-strand	322	1	40
β-strand	323-328	6	39
α-helix	330-333	4
α-helix	345-358	14
β-strand	367-372	6	39
α-helix	376-378	3
α-helix	381-384	4
β-strand	391-394	4	39
α-helix	400-416	17
β-strand	420	1	41
α-helix	426-432	7
α-helix	438-456	19
β-strand	457	1	42
β-strand	465	1	42
α-helix	469-471	3
β-strand	475	1	41
α-helix	477-483	7
α-helix	500-502	3
α-helix	512-530	19
β-strand	538-542	5	43
α-helix	550-560	11
β-strand	566-568	3	43
α-helix	570-572	3
α-helix	578-593	16
β-strand	600-602	3	43
α-helix	605-608	4
β-strand	611-612	2	44
β-strand	617-618	2	44
α-helix	621-629	9
α-helix	632-634	3
β-strand	642-644	3	43
α-helix	649-654	6
β-strand	663-666	4	43
β-strand	670	1	45
α-helix	673-683	11
α-helix	688-699	12
β-strand	705	1	45
α-helix	707-719	13
α-helix	722-724	3
α-helix	725-736	12

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	189-258	70

Chain H: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	2
β-strand	5	1	12
α-helix	19-81	63
α-helix	144-203	60

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

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)
Syntaxin-1A	G, L	protein	267	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	H	protein	222	Rattus norvegicus	P60881 (AlphaFold model)
Alpha-soluble NSF attachment protein	I, J, K	protein	296	Rattus norvegicus	P54921 (AlphaFold model)

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

>9PBV_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, L), FASTA

>9PBV_2 Syntaxin-1A (chains G, L)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 3 (H), FASTA

>9PBV_3 Synaptosomal-associated protein 25 (chains H)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

Sequence of entity 4 (I, J, K), FASTA

>9PBV_4 Alpha-soluble NSF attachment protein (chains I, J, K)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

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
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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