9PB9: Vesicle-fusing ATPase

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 8. Determined by electron microscopy at 3.45 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.45 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 12
Atoms: 41,286
Mol. weight: 690.45 kDa
Ligands: ATP, ADP
Released: 6 Aug 2025

Explore 9PB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PB9 contains 258 α-helices and 198 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	228-233	6
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	1
α-helix	267-276	10
β-strand	283-284	2	1
α-helix	287-289	3
α-helix	298-304	7
α-helix	307-313	7
β-strand	323-328	6	1
α-helix	330-332	3
α-helix	336-338	3
α-helix	348-358	11
β-strand	367-373	7	1
β-strand	386	1	2
β-strand	388	1	2
β-strand	392-394	3	1
α-helix	400-417	18
β-strand	420	1	3
α-helix	426-432	7
α-helix	438-440	3
α-helix	442-461	20
α-helix	467-473	7
β-strand	476	1	3
α-helix	479-486	8
α-helix	499-502	4
α-helix	512-530	19
β-strand	536-542	7	4
α-helix	549-559	11
β-strand	566-568	3	4
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	4
α-helix	605-608	4
β-strand	612	1	5
β-strand	617	1	5
α-helix	620-629	10
β-strand	640-646	7	4
α-helix	649-654	6
β-strand	664-666	3	4
β-strand	670	1	6
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	6
α-helix	707-717	11
α-helix	726-735	10

Chain B: 39 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
α-helix	14-18	5
β-strand	22-24	3	7
β-strand	34-40	7	7
β-strand	43-51	9	7
α-helix	56	1
β-strand	59-62	4	7
α-helix	64-70	7
β-strand	77-82	6	7
α-helix	87-90	4
β-strand	91	1	8
β-strand	94-101	8	9
α-helix	104-106	3
β-strand	111-113	3	10
α-helix	114-124	11
β-strand	128-131	4	8
β-strand	135-139	5	9
β-strand	144-153	10	9
β-strand	171	1	9
β-strand	174-177	4	8
β-strand	182-187	6	9
α-helix	188	1
β-strand	194-196	3	10
α-helix	205-207	3
β-strand	209	1	11
α-helix	215-217	3
α-helix	224-234	11
α-helix	236-238	3
α-helix	242-246	5
α-helix	251-253	3
β-strand	255-259	5	12
α-helix	266-274	9
β-strand	277	1	11
α-helix	280-282	3
β-strand	283-286	4	12
β-strand	294	1	13
α-helix	298-303	6
α-helix	304-306	3
α-helix	307-316	10
β-strand	323-328	6	12
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	12
β-strand	386	1	14
β-strand	388	1	14
β-strand	392-394	3	12
α-helix	400-409	10
α-helix	413-416	4
β-strand	420	1	15
α-helix	426-432	7
α-helix	438-454	17
α-helix	470-472	3
β-strand	475	1	15
α-helix	477-486	10
α-helix	498-502	5
α-helix	513-530	18
β-strand	538-542	5	16
α-helix	549-558	10
β-strand	566-568	3	16
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	16
α-helix	605-608	4
β-strand	612	1	17
β-strand	617	1	17
α-helix	620-629	10
β-strand	642-646	5	16
α-helix	649-654	6
β-strand	664-666	3	16
β-strand	670	1	18
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	18
α-helix	708-717	10
α-helix	722-724	3
α-helix	725-736	12

Chain C: 35 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	19
α-helix	14-19	6
β-strand	22-24	3	19
β-strand	34-40	7	19
β-strand	43-51	9	19
α-helix	56	1
β-strand	59-62	4	19
α-helix	64-70	7
β-strand	77-82	6	19
α-helix	87-90	4
β-strand	91	1	20
β-strand	94-101	8	21
β-strand	112-113	2	22
α-helix	114-124	11
β-strand	129-131	3	20
β-strand	135-140	6	21
β-strand	143-153	11	21
β-strand	171	1	21
β-strand	174-176	3	20
β-strand	182-187	6	21
α-helix	188	1
β-strand	195-196	2	22
β-strand	209	1	23
α-helix	215-218	4
α-helix	224-234	11
α-helix	242-248	7
β-strand	256-259	4	24
α-helix	267-273	7
β-strand	277	1	23
α-helix	281-282	2
β-strand	283-286	4	24
α-helix	298-303	6
α-helix	307-316	10
α-helix	317-319	3
β-strand	324-328	5	24
α-helix	330-332	3
β-strand	335	1	25
α-helix	336-338	3
α-helix	349-358	10
β-strand	368-373	6	24
β-strand	379	1	25
β-strand	391-394	4	24
α-helix	400-411	12
α-helix	414-416	3
β-strand	420	1	26
α-helix	426-432	7
α-helix	438-454	17
β-strand	458	1	27
β-strand	464	1	27
α-helix	470-472	3
β-strand	475	1	26
α-helix	477-486	10
α-helix	498-502	5
α-helix	513-530	18
β-strand	536-542	7	28
α-helix	549-558	10
β-strand	564-568	5	28
α-helix	570-572	3
α-helix	578-591	14
β-strand	597-602	6	28
α-helix	605-608	4
β-strand	612	1	29
β-strand	617	1	29
α-helix	620-629	10
β-strand	639-646	8	28
α-helix	649-654	6
β-strand	664-666	3	28
β-strand	670	1	30
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	30
α-helix	707-717	11
α-helix	726-735	10

Chain D: 38 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	31
α-helix	16-19	4
β-strand	21-24	4	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
β-strand	91	1	32
β-strand	92-100	9	33
α-helix	104-106	3
β-strand	112-113	2	34
α-helix	114-124	11
β-strand	129-131	3	32
β-strand	135-136	2	33
β-strand	139	1	35
β-strand	144	1	35
β-strand	146-154	9	33
β-strand	171	1	33
β-strand	174-176	3	32
β-strand	182-187	6	33
α-helix	188	1
β-strand	195-196	2	34
β-strand	209	1	36
α-helix	215-218	4
α-helix	224-230	7
α-helix	231-235	5
α-helix	242-248	7
α-helix	251-253	3
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
β-strand	294	1	38
α-helix	298-305	8
β-strand	323-328	6	37
α-helix	330-332	3
β-strand	335	1	39
α-helix	336	1
α-helix	346-358	13
β-strand	367-373	7	37
β-strand	379	1	39
α-helix	381-383	3
β-strand	391-394	4	37
α-helix	400-409	10
α-helix	412-417	6
β-strand	420	1	40
α-helix	426-432	7
α-helix	438-453	16
β-strand	457	1	41
β-strand	465	1	41
α-helix	470-472	3
β-strand	475	1	40
α-helix	477-486	10
α-helix	499-502	4
α-helix	513-530	18
β-strand	536-542	7	42
α-helix	549-558	10
β-strand	566-568	3	42
α-helix	570-572	3
α-helix	578-591	14
β-strand	600-602	3	42
α-helix	605-608	4
β-strand	612	1	43
β-strand	617	1	43
α-helix	621-629	9
α-helix	633-634	2
β-strand	640-646	7	42
α-helix	649-654	6
β-strand	664-666	3	42
β-strand	670	1	44
α-helix	673-683	11
α-helix	688-699	12
β-strand	705	1	44
α-helix	708-718	11
α-helix	722-724	3
α-helix	726-736	11

Chain E: 35 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	45
β-strand	7-10	4	46
α-helix	16-18	3
β-strand	22-24	3	46
β-strand	34-38	5	45
β-strand	45-48	4	45
β-strand	49-51	3	46
α-helix	56	1
β-strand	59-62	4	46
α-helix	64-70	7
β-strand	78-82	5	45
β-strand	91	1	47
β-strand	92-101	10	48
β-strand	112-113	2	49
α-helix	114-124	11
β-strand	129-131	3	47
β-strand	135-136	2	48
β-strand	139	1	50
β-strand	144	1	50
β-strand	145-154	10	48
β-strand	171	1	48
β-strand	174-176	3	47
β-strand	182-187	6	48
α-helix	188	1
β-strand	195-196	2	49
β-strand	209	1	51
α-helix	225-234	10
α-helix	236-239	4
α-helix	242-248	7
β-strand	256-259	4	52
α-helix	266-274	9
β-strand	277	1	51
α-helix	280-282	3
β-strand	283-285	3	52
β-strand	294	1	53
α-helix	298-303	6
α-helix	308-315	8
β-strand	323-327	5	52
α-helix	335-336	2
α-helix	346-358	13
β-strand	367-373	7	52
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	52
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	54
α-helix	426-432	7
α-helix	440-453	14
α-helix	454-456	3
β-strand	457-459	3	55
β-strand	463-465	3	55
β-strand	475	1	54
α-helix	477-486	10
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	56
α-helix	549-559	11
β-strand	564-568	5	56
α-helix	570-572	3
α-helix	578-590	13
β-strand	598-602	5	56
α-helix	605-608	4
β-strand	612	1	57
β-strand	617	1	57
α-helix	620-630	11
α-helix	633-634	2
β-strand	640-645	6	56
α-helix	649-654	6
β-strand	663-666	4	56
β-strand	670	1	58
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	58
α-helix	707-717	11
α-helix	725-735	11

Chain F: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	224-234	11
α-helix	236-239	4
β-strand	255-259	5	59
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-286	4	59
β-strand	294	1	60
α-helix	297-303	7
α-helix	307-316	10
α-helix	317-319	3
α-helix	320-322	3
β-strand	324-328	5	59
α-helix	330-332	3
α-helix	340-342	3
α-helix	346-358	13
β-strand	368-373	6	59
α-helix	376-378	3
α-helix	381-384	4
β-strand	391-394	4	59
α-helix	400-416	17
β-strand	420	1	61
α-helix	426-432	7
α-helix	438-454	17
β-strand	457	1	62
β-strand	465	1	62
β-strand	475	1	61
α-helix	477-486	10
α-helix	499-502	4
α-helix	513-530	18
β-strand	536-542	7	63
α-helix	550-560	11
β-strand	564-568	5	63
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	63
α-helix	605-608	4
β-strand	612	1	64
β-strand	617	1	64
α-helix	620-629	10
β-strand	639-646	8	63
α-helix	649-652	4
β-strand	663-666	4	63
β-strand	670	1	65
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	65
α-helix	707-716	10
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	13
β-strand	186	1	38
β-strand	188	1	53
β-strand	190	1	60
α-helix	198-200	3
α-helix	203-258	56

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

>9PB9_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

>9PB9_2 Syntaxin-1A (chains G, H)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 3 (I), FASTA

>9PB9_3 Synaptosomal-associated protein 25 (chains I)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

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

>9PB9_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
9PBA 3.47 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 9
9OLJ 3.52 Å, 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 18

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