9NV9: NSF Mg2+ class 1 heptamer

NSF Mg2+ class 1 heptamer. Determined by electron microscopy at 3.6 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Cricetulus griseus
Chains: 7
Atoms: 27,415
Mol. weight: 586.89 kDa
Ligands: ATP, ADP
Released: 1 Oct 2025

Explore 9NV9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NV9 contains 229 α-helices and 114 β-strands across 7 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, 16 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-239	16
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	1
α-helix	267-276	10
α-helix	279-281	3
β-strand	283-286	4	1
α-helix	287-291	5
α-helix	297-305	9
α-helix	307-313	7
β-strand	325-328	4	1
α-helix	330-333	4
α-helix	351-358	8
β-strand	369-373	5	1
α-helix	376-378	3
α-helix	381-383	3
β-strand	393-394	2	1
α-helix	401-410	10
α-helix	412-417	6
β-strand	420	1	2
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	2
α-helix	477-483	7
α-helix	496-502	7
α-helix	512-530	19
β-strand	538-542	5	3
α-helix	549-559	11
β-strand	566-568	3	3
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	3
α-helix	605-608	4
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	664-666	3	3
β-strand	670	1	5
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	5
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-734	10

Chain B: 35 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-230	7
α-helix	231-235	5
α-helix	237-239	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	6
α-helix	266-277	12
α-helix	279	1
β-strand	280-284	5	6
α-helix	287-291	5
α-helix	297-305	9
α-helix	307-315	9
α-helix	317-319	3
α-helix	320-322	3
β-strand	323-326	4	6
α-helix	351-358	8
β-strand	367-373	7	6
α-helix	376-378	3
α-helix	381-383	3
β-strand	393-394	2	6
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	7
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	7
α-helix	477-483	7
α-helix	496-502	7
α-helix	512-530	19
β-strand	538-542	5	8
α-helix	549-558	10
β-strand	565-568	4	8
α-helix	570-572	3
α-helix	578-592	15
β-strand	599-602	4	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	642-646	5	8
α-helix	649-654	6
β-strand	663-666	4	8
β-strand	670	1	10
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	10
α-helix	707-714	8
α-helix	717-719	3
α-helix	725-734	10

Chain C: 33 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-235	12
α-helix	236-239	4
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	11
α-helix	266-276	11
β-strand	283-284	2	11
α-helix	287-292	6
α-helix	297-305	9
α-helix	307-316	10
α-helix	317-319	3
α-helix	320-322	3
β-strand	323-326	4	11
α-helix	330-333	4
α-helix	351-358	8
β-strand	367-373	7	11
α-helix	376-378	3
α-helix	381-383	3
β-strand	393-394	2	11
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	12
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	12
α-helix	477-483	7
α-helix	496-502	7
α-helix	512-530	19
β-strand	538-542	5	13
α-helix	549-558	10
β-strand	566-568	3	13
α-helix	578-592	15
β-strand	600-602	3	13
α-helix	605-609	5
β-strand	612	1	14
β-strand	617	1	14
α-helix	620-629	10
α-helix	632-634	3
β-strand	642-646	5	13
α-helix	649-652	4
β-strand	665-666	2	13
α-helix	668-669	2
β-strand	670	1	15
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	15
α-helix	707-717	11
α-helix	725-734	10

Chain D: 35 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-235	12
α-helix	236-238	3
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	16
α-helix	267-276	10
α-helix	279-282	4
β-strand	283-284	2	16
α-helix	287-292	6
α-helix	297-305	9
α-helix	307-316	10
α-helix	317-319	3
α-helix	320-322	3
β-strand	323-326	4	16
α-helix	351-358	8
β-strand	367-373	7	16
α-helix	376-378	3
α-helix	381-383	3
β-strand	393-394	2	16
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	17
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	17
α-helix	477-483	7
α-helix	497-502	6
α-helix	512-530	19
β-strand	538-539	2	18
β-strand	540-542	3	19
α-helix	549-558	10
β-strand	566-568	3	18
α-helix	570-572	3
α-helix	578-591	14
α-helix	592-594	3
β-strand	600-602	3	18
α-helix	605-608	4
β-strand	612	1	20
β-strand	617	1	20
α-helix	621-629	9
α-helix	634	1
β-strand	642-643	2	18
β-strand	646	1	19
α-helix	649-652	4
β-strand	664-666	3	19
β-strand	670	1	21
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	21
α-helix	707-716	10
α-helix	717-719	3
α-helix	725-734	10

Chain E: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-239	16
α-helix	242-248	7
α-helix	251-253	3
β-strand	256-259	4	22
α-helix	267-276	10
β-strand	283-285	3	22
α-helix	287-291	5
α-helix	297-315	19
α-helix	320-322	3
β-strand	323-327	5	22
α-helix	351-358	8
β-strand	367-373	7	22
α-helix	376-378	3
α-helix	381-383	3
β-strand	392-394	3	22
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	23
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	23
α-helix	477-483	7
α-helix	496-502	7
α-helix	512-530	19
β-strand	536-542	7	24
α-helix	549-558	10
β-strand	565-568	4	24
α-helix	578-592	15
β-strand	599-602	4	24
α-helix	605-608	4
β-strand	612	1	25
β-strand	617	1	25
α-helix	620-629	10
α-helix	632-634	3
β-strand	640-646	7	24
α-helix	649-654	6
β-strand	663-666	4	24
β-strand	670	1	26
α-helix	673-683	11
α-helix	690-698	9
β-strand	705	1	26
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-734	10

Chain F: 30 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
α-helix	224-235	12
α-helix	242-246	5
α-helix	251-253	3
β-strand	255-259	5	27
α-helix	266-276	11
α-helix	279-282	4
β-strand	283-286	4	27
α-helix	287-291	5
α-helix	297-305	9
α-helix	307-316	10
α-helix	320-322	3
β-strand	323-328	6	27
α-helix	351-358	8
β-strand	367-373	7	27
α-helix	381-383	3
β-strand	392-394	3	27
α-helix	400-410	11
α-helix	412-417	6
α-helix	426-432	7
α-helix	438-457	20
α-helix	477-483	7
α-helix	497-502	6
α-helix	512-530	19
β-strand	538-542	5	28
α-helix	549-558	10
β-strand	566-568	3	28
α-helix	570-572	3
α-helix	578-592	15
β-strand	600-602	3	28
α-helix	605-608	4
β-strand	612	1	29
β-strand	617	1	29
α-helix	620-629	10
α-helix	634	1
β-strand	642-646	5	28
α-helix	649-654	6
β-strand	664-666	3	28
β-strand	670	1	30
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	30
α-helix	707-717	11
α-helix	725-734	10

Chain G: 36 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	216-218	3
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	31
α-helix	266-277	12
α-helix	281-282	2
β-strand	283-284	2	31
α-helix	287-291	5
α-helix	297-305	9
α-helix	307-313	7
α-helix	320-322	3
β-strand	323-326	4	31
α-helix	330-332	3
α-helix	351-358	8
β-strand	367-373	7	31
α-helix	376-378	3
α-helix	381-383	3
β-strand	393-394	2	31
α-helix	400-410	11
α-helix	412-417	6
β-strand	420	1	32
α-helix	426-432	7
α-helix	438-457	20
β-strand	475	1	32
α-helix	477-483	7
α-helix	496-502	7
α-helix	512-530	19
β-strand	538-539	2	33
β-strand	540-542	3	34
α-helix	549-558	10
β-strand	566-568	3	33
α-helix	570-572	3
α-helix	578-591	14
α-helix	592-594	3
β-strand	600-602	3	33
α-helix	605-609	5
β-strand	612	1	35
β-strand	617	1	35
α-helix	620-629	10
α-helix	633-634	2
β-strand	642-643	2	33
β-strand	646	1	34
α-helix	649-654	6
β-strand	664-666	3	34
α-helix	668-669	2
β-strand	670	1	36
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	36
α-helix	707-717	11
α-helix	725-734	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vesicle-fusing ATPase	A, B, C, D, E, F, G	protein	747	Cricetulus griseus	P18708 (AlphaFold model)

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

>9NV9_1 Vesicle-fusing ATPase (chains A, B, C, D, E, F, G)
GAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVP
GSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKM
AAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLV
VGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFAS
RVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGE
SEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSK
IDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGH
QLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTR
GDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLV
SVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQL
SCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEM
LNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMS
LQMDPEYRVRKFLALLREEGASPLDFD

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	7
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	7

Primary citation

SNARE disassembly requires Sec18/NSF side loading. Khan, Y.A., White, K.I., Pfuetzner, R.A. et al. Nat Struct Mol Biol (2025) 32:1708-1720. DOI 10.1038/s41594-025-01590-w · 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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