9PFF: Synaptosomal-associated protein 25

Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), non-hydrolyzing, class 27. Determined by electron microscopy at 3.09 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.09 Å
Organisms: Rattus norvegicus, Cricetulus griseus
Chains: 14
Atoms: 40,690
Mol. weight: 674.06 kDa
Ligands: ADP, ATP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PFF contains 262 α-helices and 149 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: 30 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	230-233	4
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	6
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-286	4	6
β-strand	294	1	1
α-helix	298-303	6
α-helix	304-306	3
α-helix	307-316	10
β-strand	323-328	6	6
α-helix	330-332	3
α-helix	336-338	3
α-helix	348-358	11
β-strand	367-373	7	6
α-helix	376-378	3
β-strand	391-394	4	6
α-helix	400-417	18
β-strand	420	1	7
α-helix	426-432	7
α-helix	438-462	25
α-helix	470-472	3
β-strand	475	1	7
α-helix	477-486	10
α-helix	497-502	6
α-helix	513-529	17
β-strand	536-542	7	8
α-helix	549-560	12
β-strand	564-568	5	8
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-603	7	8
α-helix	605-608	4
β-strand	612	1	9
β-strand	617	1	9
α-helix	620-629	10
α-helix	632-634	3
β-strand	639-646	8	8
α-helix	649-654	6
β-strand	664-666	3	8
β-strand	670	1	10
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	10
α-helix	707-717	11
α-helix	726-735	10

Chain B: 39 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	11
α-helix	11-12	2
α-helix	14-18	5
β-strand	22-25	4	11
β-strand	34-38	5	11
β-strand	44-52	9	11
β-strand	59-62	4	11
α-helix	64-70	7
α-helix	72-73	2
β-strand	77-82	6	11
β-strand	92-101	10	12
β-strand	111-113	3	13
α-helix	114-125	12
β-strand	129-131	3	14
β-strand	135-140	6	12
β-strand	143-153	11	12
β-strand	174-176	3	14
β-strand	177-187	11	12
α-helix	188	1
β-strand	194-196	3	13
β-strand	209	1	15
α-helix	215-217	3
α-helix	224-232	9
α-helix	242-246	5
α-helix	251-253	3
β-strand	255-259	5	16
α-helix	267-274	8
β-strand	277	1	15
α-helix	281-282	2
β-strand	283-286	4	16
β-strand	294	1	2
α-helix	298-303	6
α-helix	304-306	3
α-helix	307-316	10
β-strand	323-328	6	16
α-helix	330-332	3
α-helix	342-345	4
α-helix	347-358	12
β-strand	367-373	7	16
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	16
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	17
α-helix	426-432	7
α-helix	438-456	19
β-strand	475	1	17
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	18
α-helix	549-560	12
β-strand	564-568	5	18
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	18
α-helix	605-608	4
β-strand	612	1	19
β-strand	617	1	19
α-helix	620-629	10
α-helix	632-634	3
β-strand	639-646	8	18
α-helix	649-654	6
β-strand	664-666	3	18
α-helix	667-669	3
β-strand	670-672	3	20
α-helix	673-683	11
α-helix	689-698	10
β-strand	702-705	4	20
α-helix	707-717	11
α-helix	725-736	12

Chain C: 30 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	21
α-helix	215-218	4
α-helix	224-235	12
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	22
α-helix	267-276	10
β-strand	277	1	21
α-helix	281-282	2
β-strand	283-286	4	22
β-strand	294	1	3
α-helix	298-304	7
α-helix	307-316	10
α-helix	317-319	3
β-strand	323-328	6	22
α-helix	330-332	3
β-strand	335	1	23
α-helix	346-358	13
β-strand	367-373	7	22
α-helix	376-378	3
β-strand	379	1	23
β-strand	391-394	4	22
α-helix	400-416	17
β-strand	420	1	24
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	25
β-strand	464-465	2	25
α-helix	469-472	4
β-strand	475	1	24
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	26
α-helix	550-560	11
β-strand	564-568	5	26
α-helix	570-572	3
α-helix	578-591	14
α-helix	592-594	3
β-strand	597-602	6	26
α-helix	605-608	4
β-strand	612	1	27
β-strand	617	1	27
α-helix	620-629	10
β-strand	639-646	8	26
α-helix	649-654	6
β-strand	663-666	4	26
β-strand	670	1	28
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	28
α-helix	707-717	11
α-helix	725-736	12

Chain D: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	209	1	29
β-strand	214	1	30
α-helix	215-217	3
α-helix	224-234	11
α-helix	242-248	7
β-strand	256-259	4	31
α-helix	267-276	10
β-strand	277	1	29
α-helix	281-282	2
β-strand	283-286	4	31
β-strand	294	1	4
α-helix	297-303	7
α-helix	307-316	10
β-strand	323-328	6	31
α-helix	346-358	13
β-strand	367-373	7	31
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	31
α-helix	400-409	10
α-helix	412-416	5
β-strand	420	1	32
α-helix	426-432	7
α-helix	438-453	16
α-helix	470-472	3
β-strand	475	1	32
α-helix	477-486	10
α-helix	496-502	7
α-helix	513-530	18
β-strand	536-542	7	33
α-helix	549-560	12
β-strand	564-568	5	33
α-helix	570-572	3
α-helix	578-594	17
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
β-strand	639-646	8	33
α-helix	649-654	6
β-strand	664-666	3	33
β-strand	670	1	35
α-helix	673-683	11
α-helix	689-698	10
β-strand	705	1	35
α-helix	707-717	11
α-helix	722-724	3
α-helix	726-736	11

Chain E: 35 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	36
α-helix	14-18	5
β-strand	22-24	3	36
β-strand	34-40	7	36
β-strand	43-51	9	36
β-strand	59-62	4	36
α-helix	64-70	7
β-strand	77-82	6	36
α-helix	87-90	4
β-strand	91	1	37
β-strand	94-101	8	38
α-helix	104-106	3
β-strand	111-113	3	39
α-helix	114-125	12
β-strand	129-131	3	37
β-strand	135-140	6	38
β-strand	143-153	11	38
β-strand	174-176	3	37
β-strand	184-186	3	38
β-strand	194-196	3	39
β-strand	209	1	40
α-helix	215-218	4
α-helix	226-234	9
α-helix	236-238	3
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	283-285	3	41
β-strand	294	1	5
α-helix	297-316	20
β-strand	323-328	6	41
α-helix	330-333	4
α-helix	346-358	13
β-strand	367-373	7	41
α-helix	376-378	3
α-helix	381-383	3
β-strand	392-394	3	41
α-helix	400-416	17
β-strand	420	1	42
α-helix	426-432	7
α-helix	438-454	17
β-strand	457-458	2	43
β-strand	461	1	30
β-strand	464-465	2	43
α-helix	469-472	4
β-strand	475	1	42
α-helix	477-486	10
α-helix	496-501	6
α-helix	512-529	18
β-strand	536-542	7	44
α-helix	549-559	11
β-strand	564-568	5	44
α-helix	570-572	3
α-helix	580-594	15
β-strand	597-602	6	44
α-helix	605-608	4
β-strand	612	1	45
β-strand	617	1	45
α-helix	620-631	12
α-helix	634	1
β-strand	639-646	8	44
α-helix	649-654	6
β-strand	663-666	4	44
β-strand	670	1	46
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	46
α-helix	707-717	11
α-helix	722-736	15

Chain F: 28 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	223-229	7
α-helix	230-234	5
α-helix	242-248	7
β-strand	255-259	5	47
α-helix	265-275	11
α-helix	281-282	2
β-strand	283-286	4	47
α-helix	297-304	8
α-helix	307-315	9
β-strand	323-328	6	47
α-helix	330-333	4
α-helix	345-358	14
β-strand	367-373	7	47
α-helix	376-378	3
α-helix	382-384	3
β-strand	391-394	4	47
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-453	16
α-helix	477-486	10
α-helix	499-502	4
α-helix	513-529	17
β-strand	536-542	7	48
α-helix	550-560	11
β-strand	564-568	5	48
α-helix	570-572	3
α-helix	578-592	15
β-strand	597-602	6	48
α-helix	605-608	4
β-strand	612	1	49
β-strand	617	1	49
α-helix	620-629	10
α-helix	632-634	3
β-strand	639-645	7	48
α-helix	649-654	6
β-strand	663-666	4	48
β-strand	670	1	50
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	50
α-helix	707-717	11
α-helix	725-735	11

Chain G: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	1
β-strand	11	1	2
β-strand	13	1	3
β-strand	15	1	4
β-strand	17	1	5
α-helix	18-20	3
α-helix	28-82	55

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	193-257	65

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
Synaptosomal-associated protein 25	G, I	protein	84	Rattus norvegicus	P60881 (AlphaFold model)
Syntaxin-1A	H, J	protein	78	Rattus norvegicus	P32851 (AlphaFold model)
Alpha-soluble NSF attachment protein	L, M, N, O	protein	296	Rattus norvegicus	P54921 (AlphaFold model)
Vesicle-fusing ATPase	A, B, C, D, E, F	protein	747	Cricetulus griseus	P18708 (AlphaFold model)

Sequence of entity 1 (G, I), FASTA

>9PFF_1 Synaptosomal-associated protein 25 (chains G, I)
SMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLER
IEEGMDQINKDMKEAEKNLTDLGK

Sequence of entity 2 (H, J), FASTA

>9PFF_2 Syntaxin-1A (chains H, J)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVKYQSKARRKKIM

Sequence of entity 3 (L, M, N, O), FASTA

>9PFF_3 Alpha-soluble NSF attachment protein (chains L, M, N, O)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Sequence of entity 4 (A, B, C, D, E, F), FASTA

>9PFF_4 Vesicle-fusing ATPase (chains A, B, C, D, E, F)
GAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVP
GSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKM
AAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLV
VGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFAS
RVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGE
SEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSK
IDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGH
QLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTR
GDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLV
SVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQL
SCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEM
LNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS
LQMDPEYRVRKFLALLREEGASPLDFD

Ligands and cofactors

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

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 P60881 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1N7S 1.45 Å, High Resolution Structure of a Truncated Neuronal SNARE Complex
5W5C 1.85 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex
1JTH 2.0 Å, Crystal structure and biophysical properties of a complex between the N-terminal region…
1URQ 2.0 Å, Crystal structure of neuronal Q-SNAREs in complex with R-SNARE motif of Tomosyn
6WVW 2.11 Å, Crystal structure of the R59P-SNAP25 containing SNARE complex
1SFC 2.4 Å, Neuronal synaptic fusion complex
5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
5LOW 2.8 Å, Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)
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
5LOB 3.3 Å, Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)
9OJZ 3.39 Å, 21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 5

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