9PDD: Vesicle-fusing ATPase

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 29. Determined by electron microscopy at 4.16 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 4.16 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 11
Atoms: 40,507
Mol. weight: 637.63 kDa
Ligands: ADP, ATP, PO4, MG
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PDD contains 265 α-helices and 156 β-strands across 11 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: 31 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	215-217	3
α-helix	225-233	9
α-helix	237-239	3
α-helix	242-248	7
β-strand	256-259	4	1
α-helix	267-276	10
β-strand	283-284	2	1
α-helix	298-304	7
α-helix	307-316	10
β-strand	323-326	4	1
α-helix	330-332	3
α-helix	337-339	3
α-helix	349-358	10
β-strand	367-373	7	1
α-helix	376-378	3
α-helix	381-384	4
β-strand	394	1	1
α-helix	400-410	11
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	496-500	5
α-helix	512-529	18
β-strand	538-539	2	2
β-strand	540-542	3	3
α-helix	549-559	11
β-strand	565-568	4	2
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	2
α-helix	605-609	5
β-strand	612	1	4
β-strand	617	1	4
α-helix	620-629	10
β-strand	642-643	2	2
α-helix	649-654	6
β-strand	664-666	3	3
β-strand	670	1	5
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	5
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-735	11

Chain B: 34 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	6
α-helix	14-17	4
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
β-strand	92-101	10	7
α-helix	104-106	3
α-helix	114-125	12
β-strand	129-130	2	8
β-strand	135-139	5	7
β-strand	144-154	11	7
β-strand	171	1	7
β-strand	175-176	2	8
β-strand	177	1	7
α-helix	187-188	2
β-strand	209	1	9
α-helix	215-218	4
α-helix	225-235	11
α-helix	242-248	7
β-strand	256-259	4	10
α-helix	266-276	11
β-strand	277	1	9
α-helix	280-282	3
β-strand	283-285	3	10
β-strand	294	1	11
α-helix	298-304	7
α-helix	307-315	9
α-helix	320-322	3
β-strand	323-327	5	10
α-helix	330-332	3
β-strand	335	1	12
α-helix	347-358	12
β-strand	367-373	7	10
β-strand	379	1	12
α-helix	381-383	3
β-strand	391-394	4	10
α-helix	400-416	17
β-strand	420	1	13
α-helix	426-432	7
α-helix	438-455	18
α-helix	468-471	4
β-strand	475	1	13
α-helix	477-486	10
α-helix	498-502	5
α-helix	512-529	18
β-strand	538-542	5	14
α-helix	549-559	11
β-strand	565-568	4	14
α-helix	570-573	4
α-helix	578-593	16
β-strand	599-602	4	14
α-helix	605-608	4
β-strand	612	1	15
β-strand	617	1	15
α-helix	620-629	10
β-strand	642-646	5	14
α-helix	649-654	6
β-strand	663-666	4	14
β-strand	670	1	16
α-helix	673-683	11
α-helix	688-699	12
β-strand	705	1	16
α-helix	707-717	11
α-helix	725-735	11

Chain C: 33 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	17
α-helix	14-18	5
β-strand	22-24	3	17
β-strand	34-40	7	17
β-strand	43-51	9	17
α-helix	56	1
β-strand	59-62	4	17
α-helix	64-70	7
β-strand	77-83	7	17
β-strand	90	1	18
β-strand	92-101	10	19
α-helix	104-106	3
α-helix	114-125	12
β-strand	135-140	6	19
β-strand	143-154	12	19
β-strand	174	1	18
α-helix	187-188	2
β-strand	209	1	20
α-helix	224-234	11
α-helix	242-248	7
β-strand	256-259	4	21
α-helix	266-276	11
β-strand	277	1	20
β-strand	283-284	2	21
β-strand	294	1	22
α-helix	298-303	6
α-helix	307-315	9
β-strand	323-326	4	21
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	21
β-strand	391-394	4	21
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	23
α-helix	426-432	7
α-helix	438-454	17
α-helix	467-469	3
β-strand	475	1	23
α-helix	477-482	6
α-helix	483-487	5
α-helix	499-502	4
α-helix	513-529	17
β-strand	537-542	6	24
α-helix	550-560	11
β-strand	565-568	4	24
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	24
α-helix	605-609	5
β-strand	612	1	25
β-strand	617	1	25
α-helix	620-629	10
α-helix	633-634	2
β-strand	641-646	6	24
α-helix	649-654	6
β-strand	664-666	3	24
β-strand	670-672	3	26
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	26
α-helix	707-716	10
α-helix	725-736	12

Chain D: 39 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	27
α-helix	14-18	5
α-helix	21	1
β-strand	22-24	3	27
β-strand	34-40	7	27
β-strand	43-51	9	27
α-helix	56	1
β-strand	59-62	4	27
α-helix	64-70	7
β-strand	77-83	7	27
β-strand	94-101	8	28
α-helix	104-106	3
α-helix	114-125	12
β-strand	135-139	5	28
β-strand	144-153	10	28
β-strand	171	1	28
β-strand	185	1	29
α-helix	187-188	2
β-strand	200	1	29
β-strand	209	1	30
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	31
α-helix	267-276	10
β-strand	277	1	30
α-helix	281-282	2
β-strand	283-286	4	31
β-strand	294	1	32
α-helix	297-303	7
α-helix	304-306	3
α-helix	307-315	9
β-strand	323-328	6	31
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	31
α-helix	381-384	4
β-strand	391-394	4	31
α-helix	400-410	11
α-helix	412-415	4
α-helix	426-432	7
α-helix	438-453	16
α-helix	454-456	3
β-strand	457-458	2	33
β-strand	464-465	2	33
α-helix	469-471	3
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	34
α-helix	549-558	10
β-strand	564-567	4	34
α-helix	570-573	4
α-helix	578-592	15
β-strand	597-602	6	34
α-helix	605-608	4
α-helix	621-629	9
β-strand	639-645	7	34
α-helix	649-654	6
β-strand	665-666	2	34
β-strand	670	1	35
α-helix	673-683	11
α-helix	688-696	9
β-strand	705	1	35
α-helix	708-717	10
α-helix	725-735	11

Chain E: 36 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	36
α-helix	14-17	4
α-helix	21	1
β-strand	22-24	3	36
β-strand	34-40	7	36
β-strand	43-51	9	36
α-helix	56	1
β-strand	59-62	4	36
α-helix	64-70	7
β-strand	77-83	7	36
α-helix	87-90	4
β-strand	91	1	37
β-strand	92-101	10	38
α-helix	104-106	3
α-helix	114-125	12
β-strand	129-130	2	37
β-strand	135-140	6	38
β-strand	143-154	12	38
β-strand	171	1	38
β-strand	175-176	2	37
β-strand	185	1	39
α-helix	187-188	2
β-strand	200	1	39
α-helix	225-233	9
α-helix	237-239	3
α-helix	242-248	7
β-strand	256-259	4	40
α-helix	266-273	8
α-helix	281-282	2
β-strand	283-285	3	40
α-helix	297-315	19
β-strand	323-328	6	40
α-helix	330-332	3
α-helix	346-358	13
β-strand	367-373	7	40
α-helix	381-384	4
β-strand	391-394	4	40
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	41
α-helix	426-432	7
α-helix	438-454	17
α-helix	470-472	3
β-strand	475	1	41
α-helix	477-486	10
α-helix	498-502	5
α-helix	512-529	18
β-strand	536-542	7	42
α-helix	550-559	10
β-strand	565-568	4	42
α-helix	570-573	4
α-helix	578-592	15
β-strand	599-602	4	42
α-helix	605-608	4
β-strand	612	1	43
β-strand	617	1	43
α-helix	620-629	10
β-strand	640-645	6	42
α-helix	649-654	6
α-helix	658-660	3
β-strand	664-666	3	42
α-helix	673-683	11
α-helix	689-698	10
α-helix	707-717	11
α-helix	722-737	16

Chain F: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	215-218	4
α-helix	226-238	13
α-helix	242-248	7
α-helix	250-253	4
β-strand	256-259	4	44
α-helix	266-276	11
α-helix	280-282	3
β-strand	285	1	44
α-helix	297-299	3
α-helix	303-316	14
β-strand	326-328	3	44
α-helix	330-333	4
α-helix	346-358	13
β-strand	370-373	4	44
α-helix	382-384	3
β-strand	391-394	4	44
α-helix	400-415	16
β-strand	420	1	45
α-helix	426-432	7
α-helix	438-458	21
α-helix	468-471	4
β-strand	475	1	45
α-helix	477-486	10
α-helix	494-502	9
α-helix	512-529	18
β-strand	536-542	7	46
α-helix	550-559	10
β-strand	564-568	5	46
α-helix	570-573	4
α-helix	578-592	15
β-strand	597-602	6	46
α-helix	605-608	4
β-strand	612	1	47
β-strand	617	1	47
α-helix	620-629	10
β-strand	639-645	7	46
α-helix	649-654	6
β-strand	665-666	2	46
α-helix	668-669	2
β-strand	670	1	48
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	48
α-helix	707-719	13
α-helix	726-735	10

Chain G: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	6	1	22
β-strand	8	1	32

Chain I: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1-28	28
α-helix	34-54	21
α-helix	58-72	15
α-helix	73-75	3
α-helix	79-92	14
α-helix	98-111	14
α-helix	118-134	17
α-helix	139-154	16
α-helix	158-175	18
α-helix	178-194	17
α-helix	202-214	13
α-helix	219-231	13
α-helix	233-235	3
α-helix	239-253	15
α-helix	256-268	13
α-helix	274-285	12

3 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)
Unknown SNARE protein	G	protein	13	Rattus norvegicus
Alpha-soluble NSF attachment protein	I, J, K, L	protein	296	Rattus norvegicus	P54921 (AlphaFold model)

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

>9PDD_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), FASTA

>9PDD_2 Unknown SNARE protein (chains G)
XXXXXXXXXXXXX

Sequence of entity 3 (I, J, K, L), FASTA

>9PDD_3 Alpha-soluble NSF attachment protein (chains I, J, K, L)
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
PO4	Phosphate ion	O4 P	2
MG	Magnesium ion	Mg	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

Browse structure collections

About this viewer

MolViewer shows 9PDD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.