9PCZ: Vesicle-fusing ATPase

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 15. Determined by electron microscopy at 3.65 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 14
Atoms: 41,437
Mol. weight: 748.89 kDa
Ligands: ADP, ATP, MG, PO4
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PCZ contains 260 α-helices and 163 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: 34 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
α-helix	14-17	4
β-strand	22-24	3	1
β-strand	34-40	7	1
β-strand	43-51	9	1
α-helix	56	1
β-strand	59-62	4	1
α-helix	64-70	7
β-strand	77-83	7	1
β-strand	91	1	2
β-strand	92-101	10	3
α-helix	104-106	3
β-strand	111-113	3	4
α-helix	114-125	12
β-strand	129-131	3	2
β-strand	135-140	6	3
β-strand	143-154	12	3
β-strand	171	1	3
β-strand	174-176	3	2
β-strand	182-187	6	3
β-strand	194-196	3	4
β-strand	200	1	3
α-helix	225-233	9
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	5
α-helix	270-275	6
β-strand	283-284	2	5
α-helix	298-303	6
α-helix	307-316	10
β-strand	325-326	2	5
α-helix	330-332	3
α-helix	349-358	10
β-strand	370-373	4	5
α-helix	376-378	3
β-strand	386	1	6
β-strand	388	1	6
β-strand	394	1	5
α-helix	396-398	3
α-helix	400-409	10
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	499-502	4
α-helix	514-529	16
β-strand	537-539	3	7
β-strand	541-542	2	8
α-helix	554-559	6
β-strand	564-568	5	7
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	7
α-helix	605-608	4
β-strand	612	1	9
β-strand	617	1	9
α-helix	620-629	10
α-helix	633-634	2
β-strand	641-643	3	7
β-strand	646	1	8
α-helix	649-654	6
β-strand	665-666	2	8
α-helix	673-683	11
α-helix	689-698	10
α-helix	710-717	8
α-helix	725-735	11

Chain B: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	10
α-helix	215-217	3
α-helix	225-235	11
α-helix	236-238	3
α-helix	242-248	7
β-strand	256-259	4	11
α-helix	266-276	11
β-strand	277	1	10
α-helix	280-282	3
β-strand	283-285	3	11
β-strand	294	1	12
α-helix	298-305	8
α-helix	307-315	9
α-helix	320-322	3
β-strand	323-327	5	11
α-helix	347-358	12
β-strand	367-373	7	11
β-strand	386	1	13
β-strand	388	1	13
β-strand	391-394	4	11
α-helix	400-416	17
β-strand	420	1	14
α-helix	426-432	7
α-helix	438-454	17
α-helix	467-471	5
β-strand	475	1	14
α-helix	477-483	7
α-helix	499-502	4
α-helix	515-529	15
β-strand	538-542	5	15
α-helix	553-558	6
β-strand	566-568	3	15
α-helix	570-572	3
α-helix	578-591	14
α-helix	592-594	3
β-strand	600-602	3	15
α-helix	605-608	4
β-strand	612	1	16
β-strand	617	1	16
α-helix	620-629	10
α-helix	633-634	2
β-strand	642-646	5	15
α-helix	649-654	6
β-strand	664-666	3	15
β-strand	670	1	17
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	17
α-helix	710-717	8
α-helix	725-735	11

Chain C: 36 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	18
α-helix	14-19	6
β-strand	22-24	3	18
β-strand	34-40	7	18
β-strand	43-51	9	18
α-helix	56	1
β-strand	59-62	4	18
α-helix	64-70	7
β-strand	77-83	7	18
α-helix	87-90	4
β-strand	91	1	19
β-strand	92-101	10	20
α-helix	104-106	3
β-strand	111-113	3	21
α-helix	114-125	12
β-strand	128-131	4	19
β-strand	135-140	6	20
β-strand	143-154	12	20
β-strand	171	1	20
β-strand	174-177	4	19
β-strand	182-187	6	20
α-helix	188	1
β-strand	194-196	3	21
β-strand	200	1	20
α-helix	203-205	3
β-strand	209	1	22
α-helix	215-218	4
α-helix	224-234	11
α-helix	236-238	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	23
α-helix	268-271	4
β-strand	277	1	22
β-strand	283-285	3	23
β-strand	294	1	24
α-helix	298-305	8
α-helix	308-315	8
β-strand	323-327	5	23
α-helix	330-332	3
α-helix	347-358	12
β-strand	367-372	6	23
α-helix	381-383	3
β-strand	391-394	4	23
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	25
α-helix	426-432	7
α-helix	438-456	19
β-strand	458	1	26
β-strand	464	1	26
β-strand	475	1	25
α-helix	477-486	10
α-helix	498-500	3
α-helix	513-529	17
β-strand	537-542	6	27
α-helix	554-558	5
β-strand	565-568	4	27
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-603	5	27
α-helix	605-608	4
β-strand	612	1	28
β-strand	617	1	28
α-helix	621-628	8
α-helix	632-634	3
β-strand	641-646	6	27
α-helix	649-654	6
β-strand	665-666	2	27
β-strand	670	1	29
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	29
α-helix	725-736	12

Chain D: 36 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	30
α-helix	14-18	5
β-strand	22-24	3	30
β-strand	34-40	7	30
β-strand	43-51	9	30
α-helix	56	1
β-strand	59-62	4	30
α-helix	64-70	7
β-strand	77-83	7	30
α-helix	87-90	4
β-strand	91-101	11	31
α-helix	104-106	3
β-strand	111-113	3	32
α-helix	114-125	12
β-strand	128-131	4	31
β-strand	135-140	6	31
β-strand	143-154	12	31
β-strand	171	1	31
β-strand	174-187	14	31
α-helix	188	1
β-strand	194-196	3	32
β-strand	200	1	31
β-strand	209	1	33
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	34
α-helix	266-276	11
β-strand	277	1	33
α-helix	281-282	2
β-strand	283-286	4	34
α-helix	298-302	5
α-helix	303-306	4
α-helix	307-315	9
β-strand	323-328	6	34
α-helix	347-358	12
β-strand	367-373	7	34
α-helix	381-384	4
β-strand	391-392	2	34
α-helix	400-415	16
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	35
β-strand	464-465	2	35
α-helix	469-472	4
α-helix	477-486	10
α-helix	496-499	4
α-helix	512-514	3
α-helix	516-530	15
β-strand	536-542	7	36
α-helix	554-558	5
β-strand	564-567	4	36
α-helix	578-590	13
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
α-helix	633-634	2
β-strand	639-645	7	36
α-helix	649-654	6
β-strand	665-666	2	36
β-strand	670-672	3	38
α-helix	673-683	11
α-helix	688-696	9
β-strand	702-705	4	38
α-helix	713-719	7
α-helix	725-735	11

Chain E: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	39
α-helix	224-233	10
α-helix	237-239	3
α-helix	242-248	7
β-strand	255-259	5	40
α-helix	266-276	11
β-strand	277	1	39
β-strand	283-286	4	40
α-helix	287-289	3
α-helix	297-304	8
α-helix	308-315	8
β-strand	323-328	6	40
α-helix	346-358	13
β-strand	367-373	7	40
α-helix	381-384	4
β-strand	393-394	2	40
α-helix	400-416	17
β-strand	420	1	41
α-helix	426-432	7
α-helix	438-456	19
β-strand	458	1	42
β-strand	464	1	42
β-strand	475	1	41
α-helix	477-486	10
α-helix	497-501	5
α-helix	512-514	3
α-helix	516-529	14
β-strand	536-542	7	43
α-helix	554-559	6
β-strand	565-568	4	43
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	43
α-helix	605-608	4
β-strand	612	1	44
β-strand	617	1	44
α-helix	622-629	8
α-helix	633-634	2
β-strand	640-646	7	43
α-helix	649-654	6
β-strand	664-666	3	43
α-helix	673-683	11
α-helix	689-698	10
α-helix	710-717	8
α-helix	725-736	12

Chain F: 32 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	226-238	13
α-helix	242-248	7
β-strand	256-259	4	45
α-helix	266-276	11
α-helix	280-282	3
β-strand	283-285	3	45
α-helix	288-290	3
α-helix	297-316	20
β-strand	323	1	46
β-strand	325-328	4	45
α-helix	330-333	4
α-helix	346-359	14
β-strand	367	1	46
β-strand	370-373	4	45
α-helix	376-378	3
α-helix	382-384	3
β-strand	391-394	4	45
α-helix	400-415	16
β-strand	420	1	47
α-helix	426-432	7
α-helix	438-457	20
α-helix	468-471	4
β-strand	475	1	47
α-helix	477-486	10
α-helix	488-490	3
α-helix	495-502	8
α-helix	512-514	3
α-helix	516-529	14
β-strand	536-542	7	48
α-helix	554-559	6
β-strand	564-568	5	48
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-603	7	48
α-helix	605-608	4
β-strand	612	1	49
β-strand	617	1	49
α-helix	620-629	10
α-helix	633-634	2
β-strand	639-645	7	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	713-716	4
α-helix	717-719	3
α-helix	725-735	11

Chain I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	191	1	12
β-strand	193	1	24
α-helix	205-257	53

Chain J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	198-257	60

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

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

>9PCZ_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 (I, J), FASTA

>9PCZ_2 Syntaxin-1A (chains I, J)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 3 (K, L), FASTA

>9PCZ_3 Synaptosomal-associated protein 25 (chains K, L)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

Sequence of entity 4 (M, N, O, P), FASTA

>9PCZ_4 Alpha-soluble NSF attachment protein (chains M, N, O, P)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	7
MG	Magnesium ion	Mg	10
PO4	Phosphate ion	O4 P	2

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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