9PC3: Vesicle-fusing ATPase

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 12. Determined by electron microscopy at 3.69 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.69 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 12
Atoms: 38,755
Mol. weight: 690.45 kDa
Ligands: ATP, ADP
Released: 6 Aug 2025

Explore 9PC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PC3 contains 259 α-helices and 180 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, 16 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	224-234	11
α-helix	236-238	3
α-helix	242-248	7
α-helix	250-253	4
β-strand	255-259	5	1
α-helix	266-276	11
α-helix	279-282	4
β-strand	283-284	2	1
α-helix	297-304	8
α-helix	307-316	10
α-helix	317-319	3
β-strand	323-326	4	1
α-helix	330-332	3
β-strand	335	1	2
α-helix	348-358	11
β-strand	367-373	7	1
β-strand	379	1	2
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	477-486	10
α-helix	499-501	3
α-helix	512-529	18
β-strand	538-542	5	3
α-helix	549-560	12
β-strand	564-568	5	3
α-helix	570-572	3
α-helix	578-592	15
β-strand	598-602	5	3
β-strand	612	1	4
β-strand	617	1	4
α-helix	620-629	10
β-strand	642-646	5	3
α-helix	649-654	6
β-strand	663-666	4	3
β-strand	670	1	5
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	5
α-helix	707-718	12
α-helix	722-724	3
α-helix	725-735	11

Chain B: 42 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	6
α-helix	14-19	6
β-strand	22-24	3	6
β-strand	34-40	7	6
β-strand	43-51	9	6
α-helix	56	1
β-strand	59-62	4	6
α-helix	64-70	7
β-strand	77-83	7	6
α-helix	87-90	4
β-strand	91	1	7
β-strand	94-101	8	8
α-helix	104-106	3
β-strand	111-113	3	9
α-helix	114-124	11
β-strand	129-131	3	7
β-strand	135-140	6	8
β-strand	143-153	11	8
β-strand	174-176	3	7
β-strand	182-187	6	8
α-helix	188	1
β-strand	194-196	3	9
β-strand	209	1	10
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	11
α-helix	266-276	11
β-strand	277	1	10
α-helix	281-282	2
β-strand	283-286	4	11
α-helix	287-290	4
β-strand	294	1	12
α-helix	297-316	20
α-helix	317-319	3
α-helix	320-322	3
β-strand	323-328	6	11
α-helix	330-332	3
β-strand	335	1	13
α-helix	342-344	3
α-helix	345-358	14
β-strand	367-373	7	11
β-strand	379	1	13
α-helix	381-383	3
β-strand	386	1	14
β-strand	388	1	14
β-strand	391-394	4	11
α-helix	400-410	11
α-helix	412-416	5
β-strand	420	1	15
α-helix	426-432	7
α-helix	438-454	17
β-strand	458-459	2	16
β-strand	463-464	2	16
α-helix	467-469	3
β-strand	475	1	15
α-helix	477-486	10
α-helix	497-502	6
α-helix	512-530	19
β-strand	538-542	5	17
α-helix	549-560	12
β-strand	565-568	4	17
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	17
α-helix	605-608	4
β-strand	612	1	18
β-strand	617	1	18
α-helix	620-629	10
α-helix	633-634	2
β-strand	642-646	5	17
α-helix	649-654	6
β-strand	663-666	4	17
β-strand	670	1	19
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	19
α-helix	707-717	11
α-helix	725-736	12

Chain C: 42 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	20
α-helix	14-18	5
β-strand	22-24	3	20
β-strand	34-40	7	20
β-strand	43-51	9	20
α-helix	56	1
β-strand	59-62	4	20
α-helix	64-70	7
α-helix	72-73	2
β-strand	77-82	6	20
β-strand	91	1	21
β-strand	92-101	10	22
α-helix	104-106	3
β-strand	111-113	3	23
α-helix	114-124	11
β-strand	129-131	3	21
β-strand	135-140	6	22
β-strand	143-152	10	22
β-strand	153	1	24
β-strand	154	1	22
β-strand	171	1	24
β-strand	174-176	3	21
β-strand	182-183	2	22
β-strand	186-187	2	22
α-helix	188	1
β-strand	194-196	3	23
α-helix	205-207	3
β-strand	209	1	25
α-helix	215-218	4
α-helix	224-234	11
α-helix	236-239	4
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	26
α-helix	266-276	11
β-strand	277	1	25
α-helix	281-282	2
β-strand	283-286	4	26
β-strand	294	1	27
α-helix	297-305	9
α-helix	307-316	10
α-helix	317-319	3
β-strand	323-328	6	26
α-helix	330-332	3
β-strand	335	1	28
α-helix	336-338	3
α-helix	349-358	10
β-strand	367-373	7	26
β-strand	379	1	28
α-helix	381-383	3
β-strand	391-394	4	26
α-helix	400-415	16
β-strand	420	1	29
α-helix	426-432	7
α-helix	438-453	16
β-strand	458	1	30
β-strand	464	1	30
α-helix	467-470	4
β-strand	475	1	29
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	31
α-helix	550-560	11
β-strand	564-568	5	31
α-helix	570-573	4
α-helix	578-594	17
β-strand	597-602	6	31
α-helix	605-609	5
β-strand	612	1	32
β-strand	617	1	32
α-helix	620-629	10
α-helix	633-634	2
β-strand	639-646	8	31
α-helix	649-654	6
β-strand	664-666	3	31
α-helix	668-669	2
β-strand	670-672	3	33
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	33
α-helix	707-718	12
α-helix	722-724	3
α-helix	725-735	11

Chain D: 36 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	34
α-helix	16-18	3
β-strand	22-24	3	34
β-strand	31	1	35
β-strand	33	1	35
β-strand	34-38	5	34
β-strand	44-51	8	34
α-helix	56	1
β-strand	59-62	4	34
α-helix	64-70	7
β-strand	77-82	6	34
α-helix	84-86	3
β-strand	91	1	36
β-strand	92-100	9	37
β-strand	112-113	2	38
α-helix	114-125	12
β-strand	129-131	3	36
β-strand	135-136	2	37
β-strand	139-140	2	39
β-strand	143-144	2	39
β-strand	146-154	9	37
β-strand	171	1	37
β-strand	174-176	3	36
β-strand	182-187	6	37
β-strand	195-196	2	38
β-strand	209	1	40
α-helix	224-234	11
α-helix	236-239	4
α-helix	242-248	7
α-helix	250-253	4
β-strand	256-259	4	41
α-helix	266-276	11
β-strand	277	1	40
α-helix	281-282	2
β-strand	283-286	4	41
β-strand	294	1	42
α-helix	298-316	19
α-helix	317-319	3
β-strand	323-328	6	41
α-helix	330-332	3
α-helix	346-359	14
β-strand	367-373	7	41
α-helix	381-383	3
β-strand	391-394	4	41
α-helix	400-409	10
α-helix	412-417	6
β-strand	420	1	43
α-helix	426-432	7
α-helix	438-453	16
β-strand	458	1	44
β-strand	464	1	44
α-helix	470-472	3
β-strand	475	1	43
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	45
α-helix	549-560	12
β-strand	564-567	4	45
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	45
α-helix	605-608	4
β-strand	612	1	46
β-strand	617	1	46
α-helix	620-629	10
α-helix	632-634	3
β-strand	639-646	8	45
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	45
β-strand	670	1	47
α-helix	673-683	11
α-helix	688-699	12
β-strand	705	1	47
α-helix	709-718	10
α-helix	725-736	12

Chain E: 32 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	224-239	16
α-helix	242-248	7
α-helix	250-253	4
β-strand	255-259	5	48
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-286	4	48
β-strand	294	1	49
α-helix	297-316	20
β-strand	323-328	6	48
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	48
α-helix	376-378	3
β-strand	389-394	6	48
α-helix	396-398	3
α-helix	400-416	17
β-strand	420	1	50
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
β-strand	457-458	2	51
β-strand	464-465	2	51
α-helix	469-471	3
β-strand	475	1	50
α-helix	477-485	9
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	52
α-helix	549-559	11
β-strand	564-568	5	52
α-helix	570-572	3
α-helix	580-594	15
β-strand	597-602	6	52
α-helix	605-608	4
β-strand	612	1	53
β-strand	617	1	53
α-helix	620-631	12
α-helix	633-634	2
β-strand	639-646	8	52
α-helix	649-655	7
α-helix	658-660	3
β-strand	663-666	4	52
β-strand	670	1	54
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	54
α-helix	707-718	12
α-helix	722-724	3
α-helix	725-736	12

Chain F: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	224-233	10
α-helix	236-239	4
β-strand	256-259	4	55
α-helix	266-276	11
α-helix	280-282	3
β-strand	283-285	3	55
α-helix	297-305	9
α-helix	307-316	10
β-strand	323-328	6	55
α-helix	345-358	14
β-strand	367-373	7	55
α-helix	376-378	3
α-helix	382-384	3
β-strand	391-394	4	55
α-helix	400-417	18
β-strand	420	1	56
α-helix	426-432	7
α-helix	438-454	17
β-strand	457	1	57
β-strand	466	1	57
β-strand	475	1	56
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	58
α-helix	549-560	12
β-strand	564-568	5	58
α-helix	570-572	3
α-helix	578-594	17
β-strand	597-603	7	58
α-helix	605-608	4
β-strand	612	1	59
β-strand	617	1	59
α-helix	620-629	10
β-strand	639-646	8	58
α-helix	649-655	7
β-strand	663-666	4	58
β-strand	670-672	3	60
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	60
α-helix	707-717	11
α-helix	722-736	15

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	198-258	61

Chain H: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	182	1	12
β-strand	184	1	27
β-strand	186	1	42
β-strand	188	1	49
α-helix	197-206	10
α-helix	209-258	50

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

>9PC3_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

>9PC3_2 Syntaxin-1A (chains G, H)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 3 (I), FASTA

>9PC3_3 Synaptosomal-associated protein 25 (chains I)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

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

>9PC3_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	11
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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