9PAF: Vesicle-fusing ATPase

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 6. Determined by electron microscopy at 3.82 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.82 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 12
Atoms: 37,311
Mol. weight: 689.94 kDa
Ligands: ATP, ADP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PAF contains 246 α-helices and 141 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: 36 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	14-18	5
β-strand	22-24	3	1
β-strand	34-40	7	1
β-strand	43-51	9	1
α-helix	56	1
β-strand	59-61	3	1
α-helix	64-70	7
β-strand	77-82	6	1
α-helix	87-90	4
β-strand	91	1	2
β-strand	95-100	6	3
α-helix	104-106	3
β-strand	113	1	4
α-helix	114-124	11
β-strand	128-131	4	2
β-strand	135-140	6	3
β-strand	143-152	10	3
β-strand	172	1	3
β-strand	174-177	4	2
β-strand	185-187	3	3
α-helix	188	1
β-strand	196	1	4
α-helix	215-218	4
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	5
α-helix	267-276	10
β-strand	283-286	4	5
α-helix	287-290	4
α-helix	298-303	6
α-helix	307-316	10
α-helix	317-319	3
β-strand	325-328	4	5
α-helix	330-332	3
α-helix	336-338	3
α-helix	348-358	11
β-strand	369-373	5	5
β-strand	392-394	3	5
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-462	25
α-helix	467-471	5
α-helix	473-475	3
α-helix	477-486	10
α-helix	497-502	6
α-helix	513-529	17
β-strand	536-542	7	6
α-helix	549-560	12
β-strand	566-568	3	6
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	6
β-strand	612	1	7
β-strand	617	1	7
α-helix	620-629	10
α-helix	632-634	3
β-strand	640-646	7	6
α-helix	649-654	6
β-strand	664-666	3	6
α-helix	673-683	11
α-helix	688-697	10
α-helix	707-717	11
α-helix	726-735	10

Chain B: 33 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	8
α-helix	215-218	4
α-helix	224-230	7
α-helix	231-235	5
α-helix	236-238	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	9
α-helix	267-276	10
β-strand	277	1	8
α-helix	280-282	3
β-strand	283-285	3	9
α-helix	298-303	6
α-helix	307-315	9
β-strand	325-327	3	9
α-helix	330-332	3
β-strand	335	1	10
α-helix	351-358	8
β-strand	369-373	5	9
α-helix	376-378	3
β-strand	379	1	10
β-strand	391-394	4	9
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	11
α-helix	426-432	7
α-helix	438-459	22
β-strand	475	1	11
α-helix	477-482	6
α-helix	483-487	5
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	12
α-helix	549-559	11
β-strand	565-568	4	12
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	12
α-helix	605-609	5
β-strand	612	1	13
β-strand	617	1	13
α-helix	620-629	10
α-helix	633-634	2
β-strand	640-646	7	12
α-helix	649-654	6
β-strand	664-666	3	12
α-helix	668-669	2
β-strand	670	1	14
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	14
α-helix	707-717	11
α-helix	725-736	12

Chain C: 37 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	15
α-helix	14-18	5
β-strand	21-24	4	15
β-strand	34-40	7	15
β-strand	43-51	9	15
α-helix	56	1
β-strand	60-62	3	15
α-helix	64-70	7
β-strand	79-83	5	15
β-strand	95-101	7	16
α-helix	104-106	3
β-strand	111-113	3	17
α-helix	114-124	11
β-strand	129-131	3	18
β-strand	135-139	5	16
β-strand	144-152	9	16
β-strand	174-176	3	18
β-strand	183-187	5	16
α-helix	188	1
β-strand	194-196	3	17
β-strand	209	1	19
α-helix	215-218	4
α-helix	224-230	7
α-helix	231-235	5
α-helix	236-238	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	20
α-helix	267-275	9
β-strand	277	1	19
α-helix	281-282	2
β-strand	283-286	4	20
β-strand	294	1	21
α-helix	298-304	7
α-helix	307-316	10
β-strand	323-328	6	20
α-helix	330-332	3
β-strand	335	1	22
α-helix	336-337	2
α-helix	349-358	10
β-strand	367-373	7	20
β-strand	379	1	22
α-helix	381-384	4
β-strand	391-394	4	20
α-helix	400-416	17
β-strand	420	1	23
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	24
β-strand	464-465	2	24
α-helix	470-472	3
β-strand	475	1	23
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-527	16
β-strand	536-542	7	25
α-helix	550-560	11
β-strand	564-568	5	25
α-helix	570-572	3
α-helix	578-591	14
β-strand	598-602	5	25
α-helix	605-607	3
β-strand	612	1	26
β-strand	617	1	26
α-helix	620-628	9
β-strand	640-646	7	25
α-helix	649-654	6
β-strand	663-666	4	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	725-736	12

Chain D: 31 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	28
α-helix	215-218	4
α-helix	224-230	7
α-helix	231-235	5
α-helix	242-248	7
β-strand	256-259	4	29
α-helix	266-276	11
β-strand	277	1	28
α-helix	281-282	2
β-strand	283-286	4	29
β-strand	294	1	30
α-helix	298-305	8
α-helix	307-316	10
β-strand	323-328	6	29
α-helix	347-358	12
β-strand	367-372	6	29
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	29
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	31
α-helix	426-432	7
α-helix	440-453	14
α-helix	454-456	3
β-strand	457-458	2	32
β-strand	464-465	2	32
β-strand	475	1	31
α-helix	477-482	6
α-helix	483-487	5
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	33
α-helix	549-560	12
β-strand	564-568	5	33
α-helix	570-572	3
α-helix	578-591	14
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
α-helix	632-635	4
β-strand	639-646	8	33
α-helix	649-654	6
β-strand	663-665	3	33
β-strand	670	1	35
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	35
α-helix	707-718	12
α-helix	725-736	12

Chain E: 30 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	36
α-helix	215-218	4
α-helix	224-235	12
α-helix	236-238	3
α-helix	242-248	7
β-strand	256-259	4	37
α-helix	266-276	11
β-strand	277	1	36
α-helix	281-282	2
β-strand	283-286	4	37
α-helix	297-316	20
α-helix	320-322	3
β-strand	323-328	6	37
α-helix	330-333	4
α-helix	348-358	11
β-strand	367-373	7	37
α-helix	376-378	3
β-strand	391-394	4	37
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	38
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
β-strand	458	1	39
β-strand	464	1	39
α-helix	470-472	3
β-strand	475	1	38
α-helix	477-486	10
α-helix	512-529	18
β-strand	536-542	7	40
α-helix	549-559	11
β-strand	564-568	5	40
α-helix	570-572	3
α-helix	580-594	15
β-strand	598-602	5	40
α-helix	606-608	3
β-strand	612	1	41
β-strand	617	1	41
α-helix	620-629	10
α-helix	633-634	2
β-strand	640-646	7	40
α-helix	649-654	6
β-strand	663-666	4	40
β-strand	670	1	42
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	42
α-helix	707-717	11
α-helix	722-736	15

Chain F: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	224-235	12
α-helix	242-248	7
β-strand	258	1	43
α-helix	265-276	12
α-helix	281-282	2
β-strand	283-286	4	43
α-helix	297-316	20
α-helix	320-322	3
β-strand	323-328	6	43
α-helix	330-332	3
α-helix	345-358	14
β-strand	367-372	6	43
α-helix	376-378	3
α-helix	382-384	3
α-helix	400-417	18
α-helix	426-432	7
α-helix	438-456	19
α-helix	469-471	3
α-helix	477-484	8
α-helix	500-502	3
α-helix	513-530	18
β-strand	536-542	7	44
α-helix	550-560	11
β-strand	564-568	5	44
α-helix	570-572	3
α-helix	578-593	16
β-strand	598-602	5	44
α-helix	605-608	4
β-strand	611-612	2	45
β-strand	617-618	2	45
α-helix	620-629	10
β-strand	640-646	7	44
α-helix	649-654	6
β-strand	664-666	3	44
β-strand	670	1	46
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	46
α-helix	707-718	12
α-helix	725-736	12

Chain G: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	180	1	21
β-strand	182	1	30
α-helix	193-199	7
α-helix	202-258	57

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	198-258	61

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

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

>9PAF_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, H), FASTA

>9PAF_2 Syntaxin-1A (chains G, H)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 3 (I), FASTA

>9PAF_3 Synaptosomal-associated protein 25 (chains I)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

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

>9PAF_4 Alpha-soluble NSF attachment protein (chains J, K, L)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Ligands and cofactors

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

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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