3J97: Vesicle-fusing ATPase

Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State II). Determined by electron microscopy at 7.8 Å resolution. Released 28 Jan 2015.

Method: Electron microscopy
Resolution: 7.8 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 13
Atoms: 41,095
Mol. weight: 668.6 kDa
Released: 28 Jan 2015

Explore 3J97 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J97 contains 254 α-helices and 197 β-strands across 13 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, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	8-10	3	2
β-strand	22-24	3	2
β-strand	34-40	7	1
β-strand	43-48	6	1
β-strand	49-51	3	2
β-strand	60-62	3	2
α-helix	64-69	6
β-strand	77-82	6	1
β-strand	91-99	9	3
β-strand	101	1	3
β-strand	111-113	3	4
α-helix	114-124	11
β-strand	128-131	4	3
β-strand	135-140	6	3
β-strand	143-154	12	3
β-strand	171	1	3
β-strand	174-187	14	3
α-helix	188	1
β-strand	194-196	3	4
α-helix	224-239	16
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	5
α-helix	261	1
α-helix	266-277	12
β-strand	283-285	3	5
α-helix	297-315	19
β-strand	323-328	6	5
α-helix	349-358	10
β-strand	367-372	6	5
α-helix	381-384	4
β-strand	391-394	4	5
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	480-488	9
α-helix	499-503	5
α-helix	512-530	19
β-strand	536-542	7	6
α-helix	549-560	12
β-strand	564-567	4	6
α-helix	570-573	4
α-helix	578-594	17
β-strand	597-602	6	6
α-helix	605-609	5
β-strand	612	1	7
β-strand	617	1	7
α-helix	620-631	12
α-helix	633-634	2
β-strand	639-646	8	6
α-helix	649-655	7
α-helix	657-660	4
β-strand	663-666	4	6
β-strand	670	1	8
α-helix	673-683	11
α-helix	688-698	11
β-strand	705	1	8
α-helix	707-718	12
α-helix	722-735	14

Chain B: 30 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	8-10	3	10
β-strand	22	1	11
β-strand	23	1	10
β-strand	34-40	7	9
β-strand	43-48	6	9
β-strand	49	1	11
α-helix	56	1
β-strand	60-62	3	10
α-helix	64-70	7
β-strand	77-80	4	9
β-strand	82-83	2	9
β-strand	91	1	12
β-strand	92-99	8	13
β-strand	100	1	14
β-strand	112-113	2	15
α-helix	114-122	9
β-strand	128-131	4	12
β-strand	135-139	5	14
β-strand	144-148	5	14
β-strand	149-154	6	13
β-strand	171	1	13
β-strand	174-177	4	12
β-strand	182-187	6	13
β-strand	195-196	2	15
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	16
α-helix	266-277	12
β-strand	284-286	3	16
α-helix	298-316	19
β-strand	323-328	6	16
α-helix	349-358	10
β-strand	367-373	7	16
α-helix	381-384	4
β-strand	391-394	4	16
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	481-488	8
α-helix	498-501	4
α-helix	512-530	19
β-strand	536-542	7	17
α-helix	549-560	12
β-strand	564-568	5	17
α-helix	578-594	17
β-strand	597-602	6	17
α-helix	605-608	4
α-helix	620-631	12
α-helix	634-635	2
β-strand	639-646	8	17
α-helix	649-655	7
α-helix	657-660	4
β-strand	663-666	4	17
α-helix	668-669	2
β-strand	670-672	3	18
α-helix	673-683	11
α-helix	688-696	9
β-strand	702-705	4	18
α-helix	708-718	11
α-helix	725-733	9

Chain C: 32 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	19
α-helix	16-18	3
β-strand	22-24	3	19
β-strand	34-38	5	19
β-strand	44-51	8	19
α-helix	56	1
β-strand	59-62	4	19
α-helix	64-69	6
β-strand	77-82	6	19
β-strand	91-99	9	20
β-strand	101	1	21
α-helix	104-106	3
β-strand	111-113	3	22
α-helix	115-122	8
β-strand	128-131	4	20
β-strand	135-140	6	21
β-strand	143-148	6	21
β-strand	149-153	5	20
β-strand	171	1	20
β-strand	174-187	14	20
β-strand	194-196	3	22
α-helix	225-239	15
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	23
α-helix	266-277	12
β-strand	284-286	3	23
α-helix	298-316	19
β-strand	323-328	6	23
α-helix	330-333	4
α-helix	349-358	10
β-strand	367-373	7	23
α-helix	381-384	4
β-strand	391-394	4	23
α-helix	395-399	5
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	481-488	8
α-helix	499-502	4
α-helix	512-530	19
β-strand	536-542	7	24
α-helix	549-560	12
β-strand	564-568	5	24
α-helix	578-594	17
β-strand	597-602	6	24
α-helix	605-609	5
β-strand	612	1	25
β-strand	617	1	25
α-helix	620-631	12
α-helix	634	1
β-strand	639-646	8	24
α-helix	649-655	7
α-helix	657-660	4
β-strand	663-666	4	24
α-helix	668-669	2
β-strand	670-672	3	26
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	26
α-helix	707-719	13
α-helix	726-736	11

Chain D: 33 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	27
α-helix	16-18	3
β-strand	22	1	28
β-strand	23	1	27
β-strand	34-40	7	27
β-strand	43-48	6	27
β-strand	49	1	28
α-helix	56	1
β-strand	59-62	4	27
α-helix	64-66	3
α-helix	67-71	5
β-strand	77-83	7	27
β-strand	91-97	7	29
β-strand	101	1	30
β-strand	112-113	2	31
α-helix	114-121	8
β-strand	128-131	4	29
β-strand	135	1	32
β-strand	138-139	2	30
β-strand	144-145	2	30
β-strand	148	1	32
β-strand	149-154	6	29
β-strand	171	1	29
β-strand	174-185	12	29
β-strand	195-196	2	31
α-helix	224-239	16
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	33
α-helix	266-277	12
β-strand	284-286	3	33
α-helix	296-316	21
β-strand	323-328	6	33
α-helix	349-356	8
β-strand	367-373	7	33
α-helix	381-384	4
β-strand	391-394	4	33
α-helix	395-396	2
α-helix	398-399	2
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	481-487	7
α-helix	499-501	3
α-helix	512-530	19
β-strand	536-542	7	34
α-helix	549-558	10
β-strand	564-568	5	34
α-helix	570-573	4
α-helix	578-592	15
β-strand	597-602	6	34
α-helix	605-609	5
β-strand	612	1	35
β-strand	617	1	35
α-helix	620-631	12
α-helix	634-635	2
β-strand	639-645	7	34
α-helix	649-655	7
α-helix	658-660	3
β-strand	663-666	4	34
α-helix	668-669	2
β-strand	670-672	3	36
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	36
α-helix	707-717	11
α-helix	726-735	10

Chain E: 31 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	8-10	3	38
α-helix	14-16	3
β-strand	22-24	3	38
β-strand	34-40	7	37
β-strand	43-48	6	37
β-strand	49-51	3	38
α-helix	56	1
β-strand	60-62	3	38
α-helix	64-66	3
α-helix	67-71	5
β-strand	77-82	6	37
β-strand	91-99	9	39
β-strand	101	1	40
β-strand	111-113	3	41
α-helix	115-122	8
β-strand	128-131	4	39
β-strand	135-139	5	40
β-strand	144-148	5	40
β-strand	149-154	6	39
β-strand	171	1	39
β-strand	174-187	14	39
β-strand	194-196	3	41
α-helix	225-239	15
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	42
α-helix	266-277	12
β-strand	284-286	3	42
α-helix	298-316	19
β-strand	323-328	6	42
α-helix	349-358	10
β-strand	367-373	7	42
α-helix	381-384	4
β-strand	391-394	4	42
α-helix	395-399	5
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	480-487	8
α-helix	512-529	18
β-strand	536-542	7	43
α-helix	549-560	12
β-strand	564-566	3	43
α-helix	570-573	4
α-helix	578-594	17
β-strand	598-603	6	43
α-helix	605-609	5
β-strand	612	1	44
β-strand	617	1	44
α-helix	620-631	12
α-helix	634-635	2
β-strand	640-646	7	43
α-helix	649-654	6
α-helix	657-660	4
β-strand	663-666	4	43
α-helix	668-669	2
β-strand	670-672	3	45
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	45
α-helix	707-718	12
α-helix	722-736	15

Chain F: 25 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	46
β-strand	8-10	3	47
β-strand	22-24	3	47
β-strand	31	1	48
β-strand	33	1	48
β-strand	34-38	5	46
β-strand	44-48	5	46
β-strand	49-51	3	47
β-strand	60-62	3	47
α-helix	64-70	7
β-strand	77-82	6	46
β-strand	91-99	9	49
β-strand	101	1	50
β-strand	111-113	3	51
α-helix	114-122	9
β-strand	128-131	4	49
β-strand	135-139	5	50
β-strand	144-148	5	50
β-strand	149-154	6	49
β-strand	171	1	49
β-strand	174-187	14	49
β-strand	194-196	3	51
α-helix	225-239	15
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	52
α-helix	266-277	12
β-strand	284-286	3	52
α-helix	298-316	19
β-strand	323-328	6	52
α-helix	349-358	10
β-strand	367-373	7	52
α-helix	381-384	4
β-strand	391-394	4	52
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	499-502	4
α-helix	512-530	19
β-strand	536-542	7	53
α-helix	549-560	12
β-strand	564-568	5	53
α-helix	578-594	17
β-strand	597-602	6	53
α-helix	605-609	5
β-strand	612	1	54
β-strand	617	1	54
α-helix	620-631	12
α-helix	634-635	2
β-strand	639-646	8	53
α-helix	649-655	7
α-helix	657-660	4
β-strand	665-666	2	53
β-strand	670-672	3	55
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	55
α-helix	707-717	11
α-helix	724-735	12

Chain G: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	26-29	4
α-helix	35-54	20
α-helix	59-73	15
α-helix	78-93	16
α-helix	102-114	13
α-helix	117-133	17
α-helix	138-154	17
α-helix	158-172	15
α-helix	178-190	13
α-helix	202-211	10
α-helix	220-227	8
α-helix	237-239	3
α-helix	241-249	9
α-helix	259-269	11
α-helix	271-273	3
α-helix	274-291	18

Chain H: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	30	1	56
β-strand	32	1	56
α-helix	35-54	20
α-helix	59-75	17
α-helix	78-93	16
α-helix	100-114	15
α-helix	117-133	17
α-helix	138-154	17
α-helix	158-174	17
α-helix	178-193	16
α-helix	202-211	10
α-helix	222-226	5
α-helix	237-239	3
α-helix	241-251	11
α-helix	258-269	12
α-helix	271-273	3
α-helix	274-291	18

5 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)
Alpha-soluble NSF attachment protein	G, H, I, J	protein	297	Rattus norvegicus	P54921 (AlphaFold model)
Vesicle-associated membrane protein 2	K	protein	63	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	L	protein	67	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	M	protein	198	Rattus norvegicus	P60881

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

>3J97_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, I, J), FASTA

>3J97_2 Alpha-soluble NSF attachment protein (chains G, H, I, J)
GSMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNW
SAAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFT
IAAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQY
QKAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDS
RECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Sequence of entity 3 (K), FASTA

>3J97_3 Vesicle-associated membrane protein 2 (chains K)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW

Sequence of entity 4 (L), FASTA

>3J97_4 Syntaxin-1A (chains L)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK

Sequence of entity 5 (M), FASTA

>3J97_5 Synaptosomal-associated protein 25 (chains M)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGKFCGLCVCPCNKLKSSDAYKKAWGNNQDGVVASQPARVVDEREQ
MAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKAD
SNKTRIDEANQRATKMLG

Primary citation

Mechanistic insights into the recycling machine of the SNARE complex. Zhao, M., Wu, S., Zhou, Q. et al. Nature (2015) 518:61-67. DOI 10.1038/nature14148 · 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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