9PD1: Vesicle-fusing ATPase

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 20. Determined by electron microscopy at 4.5 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 14
Atoms: 42,293
Mol. weight: 748.31 kDa
Ligands: ATP, ADP
Released: 6 Aug 2025

Explore 9PD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PD1 contains 269 α-helices and 167 β-strands across 14 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
β-strand	218	1	1
β-strand	220	1	1
α-helix	225-234	10
α-helix	242-248	7
β-strand	255-259	5	2
α-helix	266-276	11
β-strand	283-284	2	2
α-helix	298-303	6
α-helix	304-306	3
α-helix	307-316	10
β-strand	323-326	4	2
α-helix	330-332	3
α-helix	349-358	10
β-strand	367-373	7	2
α-helix	382-384	3
β-strand	394	1	2
α-helix	400-410	11
α-helix	412-417	6
α-helix	427-432	6
α-helix	438-462	25
α-helix	467-471	5
α-helix	478-486	9
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	3
α-helix	549-559	11
β-strand	564-568	5	3
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	3
α-helix	605-609	5
β-strand	612	1	4
β-strand	617	1	4
α-helix	620-629	10
β-strand	640-646	7	3
α-helix	649-654	6
β-strand	664-666	3	3
β-strand	670	1	5
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	5
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-735	11

Chain B: 30 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	6
α-helix	215-218	4
α-helix	225-234	10
α-helix	236-238	3
α-helix	242-248	7
β-strand	256-259	4	7
α-helix	266-276	11
β-strand	277	1	6
β-strand	283-285	3	7
α-helix	298-304	7
α-helix	307-315	9
α-helix	320-322	3
β-strand	323-328	6	7
α-helix	330-332	3
α-helix	346-357	12
β-strand	367-373	7	7
α-helix	376-378	3
α-helix	381-383	3
β-strand	385	1	8
β-strand	388	1	8
β-strand	391-394	4	7
α-helix	400-416	17
β-strand	420	1	9
α-helix	426-432	7
α-helix	438-456	19
α-helix	467-471	5
β-strand	475	1	9
α-helix	477-486	10
α-helix	498-502	5
α-helix	512-530	19
β-strand	538-542	5	10
α-helix	549-558	10
β-strand	565-568	4	10
α-helix	570-573	4
α-helix	578-592	15
β-strand	599-602	4	10
α-helix	605-609	5
β-strand	612	1	11
β-strand	617	1	11
α-helix	620-629	10
β-strand	642-646	5	10
α-helix	649-654	6
α-helix	657-659	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	725-735	11

Chain C: 38 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	13
α-helix	14-18	5
β-strand	22-24	3	13
β-strand	34-40	7	13
β-strand	43-51	9	13
α-helix	56	1
β-strand	59-62	4	13
α-helix	64-70	7
β-strand	77-83	7	13
α-helix	87-90	4
β-strand	91-101	11	14
α-helix	104-106	3
β-strand	112-113	2	15
α-helix	114-125	12
β-strand	128-131	4	14
β-strand	135-139	5	14
β-strand	144-154	11	14
β-strand	171-172	2	14
β-strand	174-187	14	14
α-helix	188	1
β-strand	195-196	2	15
β-strand	209	1	16
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-248	7
β-strand	256-259	4	17
α-helix	266-276	11
β-strand	277	1	16
α-helix	282	1
β-strand	283-285	3	17
α-helix	298-305	8
α-helix	307-316	10
β-strand	324-327	4	17
α-helix	330-332	3
α-helix	346-358	13
β-strand	368-373	6	17
α-helix	381-383	3
β-strand	391-394	4	17
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	496-500	5
α-helix	512-529	18
β-strand	537-542	6	19
α-helix	549-558	10
β-strand	564-568	5	19
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	19
α-helix	605-609	5
β-strand	612	1	20
β-strand	617	1	20
α-helix	620-629	10
α-helix	632-634	3
β-strand	641-645	5	19
α-helix	649-654	6
α-helix	657-659	3
β-strand	664-666	3	19
β-strand	670	1	21
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	21
α-helix	707-717	11
α-helix	725-736	12

Chain D: 37 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	22
α-helix	14-18	5
β-strand	22-24	3	22
β-strand	34-40	7	22
β-strand	43-51	9	22
α-helix	56	1
β-strand	59-62	4	22
α-helix	64-70	7
β-strand	77-82	6	22
α-helix	87-90	4
β-strand	91	1	23
β-strand	92-101	10	24
α-helix	104-106	3
β-strand	112-113	2	25
α-helix	114-125	12
β-strand	128-131	4	23
β-strand	135-140	6	24
β-strand	143-154	12	24
β-strand	171	1	24
β-strand	174-177	4	23
β-strand	182-185	4	24
α-helix	187-188	2
β-strand	195-196	2	25
β-strand	200	1	24
β-strand	209	1	26
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-246	5
α-helix	250-253	4
β-strand	255-259	5	27
α-helix	266-276	11
β-strand	277	1	26
α-helix	280-282	3
β-strand	283-285	3	27
α-helix	297-304	8
α-helix	307-315	9
α-helix	320-322	3
β-strand	323-328	6	27
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	27
α-helix	382-384	3
β-strand	391-392	2	27
α-helix	400-409	10
α-helix	415-417	3
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	28
β-strand	464-465	2	28
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	29
α-helix	549-558	10
β-strand	564-568	5	29
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	29
α-helix	605-608	4
α-helix	620-629	10
β-strand	639-646	8	29
α-helix	649-654	6
β-strand	664-666	3	29
β-strand	670	1	30
α-helix	673-683	11
α-helix	688-696	9
β-strand	705	1	30
α-helix	707-718	12
α-helix	725-735	11

Chain E: 34 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	31
α-helix	14-18	5
β-strand	22-24	3	31
β-strand	34-40	7	31
β-strand	43-51	9	31
α-helix	56	1
β-strand	59-62	4	31
α-helix	64-70	7
β-strand	77-82	6	31
α-helix	87-90	4
β-strand	91	1	32
β-strand	92-101	10	33
α-helix	104-106	3
β-strand	112-113	2	34
α-helix	114-125	12
β-strand	129-131	3	32
β-strand	135-139	5	33
β-strand	144-154	11	33
β-strand	171-172	2	33
β-strand	174-176	3	32
β-strand	182-185	4	33
α-helix	187-188	2
β-strand	195-196	2	34
β-strand	200	1	33
α-helix	224-233	10
α-helix	237-239	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-257	3	35
β-strand	258-259	2	36
α-helix	270-273	4
α-helix	281-282	2
β-strand	283-285	3	35
α-helix	297-315	19
β-strand	323-327	5	35
α-helix	330-333	4
α-helix	346-358	13
β-strand	367-371	5	35
α-helix	382-384	3
β-strand	393-394	2	36
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	37
α-helix	426-432	7
α-helix	438-455	18
β-strand	457	1	38
β-strand	465	1	38
β-strand	475	1	37
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	39
α-helix	549-559	11
β-strand	565-568	4	39
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	39
α-helix	605-608	4
β-strand	612	1	40
β-strand	617	1	40
α-helix	620-629	10
β-strand	640-646	7	39
α-helix	649-654	6
β-strand	663-666	4	39
α-helix	673-683	11
α-helix	689-698	10
α-helix	707-717	11
α-helix	725-737	13

Chain F: 37 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	41
α-helix	14-18	5
α-helix	21	1
β-strand	22-24	3	41
β-strand	34-40	7	41
β-strand	43-51	9	41
α-helix	56	1
β-strand	59-62	4	41
α-helix	64-70	7
β-strand	77-83	7	41
α-helix	87-90	4
β-strand	91	1	42
β-strand	92-101	10	43
α-helix	104-106	3
β-strand	112-113	2	44
α-helix	114-125	12
β-strand	128-131	4	42
β-strand	135-139	5	43
β-strand	144-154	11	43
β-strand	171	1	43
β-strand	174-177	4	42
β-strand	182-185	4	43
α-helix	187-188	2
β-strand	195-196	2	44
α-helix	215-218	4
α-helix	226-238	13
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-257	2	45
β-strand	259	1	46
α-helix	266-276	11
α-helix	280-282	3
α-helix	288-290	3
α-helix	297-316	20
α-helix	321-323	3
β-strand	326-328	3	45
α-helix	330-333	4
α-helix	346-359	14
β-strand	370-372	3	45
α-helix	382-384	3
β-strand	394	1	46
α-helix	400-415	16
β-strand	420	1	47
α-helix	426-432	7
α-helix	438-458	21
α-helix	468-471	4
β-strand	475	1	47
α-helix	477-486	10
α-helix	495-502	8
α-helix	512-529	18
β-strand	536-542	7	48
α-helix	549-559	11
β-strand	564-568	5	48
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	48
α-helix	605-608	4
β-strand	612	1	49
β-strand	617	1	49
α-helix	620-629	10
β-strand	639-646	8	48
α-helix	649-654	6
β-strand	665-666	2	48
β-strand	670	1	50
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	50
α-helix	707-718	12
α-helix	726-735	10

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	202-257	56

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	195-257	63

6 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)
Synaptosomal-associated protein 25	I, J	protein	222	Rattus norvegicus	P60881 (AlphaFold model)
Syntaxin-1A	G, H	protein	267	Rattus norvegicus	P32851 (AlphaFold model)
Alpha-soluble NSF attachment protein	K, L, M, N	protein	296	Rattus norvegicus	P54921 (AlphaFold model)

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

>9PD1_1 Vesicle-fusing ATPase (chains A, B, C, D, E, F)
GANMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVP
GSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKM
AAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLV
VGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFAS
RVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGE
SEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSK
IDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGH
QLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTR
GDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLV
SVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQL
SCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEM
LNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS
LQMDPEYRVRKFLALLREEGASPLDFD

Sequence of entity 2 (I, J), FASTA

>9PD1_2 Synaptosomal-associated protein 25 (chains I, J)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

Sequence of entity 3 (G, H), FASTA

>9PD1_3 Syntaxin-1A (chains G, H)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 4 (K, L, M, N), FASTA

>9PD1_4 Alpha-soluble NSF attachment protein (chains K, L, M, N)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Ligands and cofactors

ID	Name	Formula	Copies
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
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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