3J99: Vesicle-fusing ATPase

Structure of 20S supercomplex determined by single particle cryoelectron microscopy (State IIIb). Determined by electron microscopy at 8.2 Å resolution. Released 28 Jan 2015.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 13
Atoms: 40,976
Mol. weight: 667.28 kDa
Released: 28 Jan 2015

Explore 3J99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J99 contains 257 α-helices and 202 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, 34 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
α-helix	56	1
β-strand	60-62	3	2
α-helix	64-69	6
β-strand	77-83	7	1
β-strand	91	1	3
β-strand	92-99	8	4
β-strand	101	1	5
β-strand	111-113	3	6
α-helix	114-122	9
β-strand	128-131	4	3
β-strand	135-140	6	5
β-strand	143-148	6	5
β-strand	149-154	6	4
β-strand	171-172	2	4
β-strand	174-177	4	3
β-strand	182-187	6	4
β-strand	194-196	3	6
α-helix	224-239	16
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	7
α-helix	261	1
α-helix	266-277	12
β-strand	283-285	3	7
α-helix	297-315	19
β-strand	323-328	6	7
α-helix	349-358	10
β-strand	367-372	6	7
α-helix	381-384	4
β-strand	391-394	4	7
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	8
α-helix	549-560	12
β-strand	564-567	4	8
α-helix	570-573	4
α-helix	578-594	17
β-strand	597-602	6	8
α-helix	605-609	5
β-strand	612	1	9
β-strand	617	1	9
α-helix	620-631	12
α-helix	633-634	2
β-strand	639-646	8	8
α-helix	649-655	7
α-helix	657-660	4
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	707-718	12
α-helix	722-735	14

Chain B: 33 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	8-10	3	12
α-helix	15-18	4
β-strand	22	1	13
β-strand	23	1	12
β-strand	31	1	14
β-strand	33	1	14
β-strand	34-38	5	11
β-strand	44-48	5	11
β-strand	49	1	13
α-helix	55-56	2
β-strand	60-62	3	12
α-helix	64-69	6
β-strand	77-83	7	11
β-strand	91-99	9	15
β-strand	101	1	16
β-strand	111-113	3	17
α-helix	114-122	9
β-strand	128-131	4	15
β-strand	135-140	6	16
β-strand	143-148	6	16
β-strand	149-154	6	15
β-strand	170-171	2	15
β-strand	174-187	14	15
α-helix	188	1
β-strand	194-196	3	17
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	18
α-helix	266-277	12
β-strand	284-286	3	18
α-helix	298-316	19
β-strand	323-328	6	18
α-helix	349-358	10
β-strand	367-373	7	18
α-helix	381-384	4
β-strand	391-394	4	18
α-helix	397-399	3
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-456	19
α-helix	480-487	8
α-helix	497-501	5
α-helix	512-530	19
β-strand	536-542	7	19
α-helix	549-560	12
β-strand	564-568	5	19
α-helix	578-594	17
β-strand	597-602	6	19
α-helix	605-608	4
α-helix	620-631	12
α-helix	634-635	2
β-strand	639-646	8	19
α-helix	649-655	7
α-helix	657-660	4
β-strand	663-666	4	19
α-helix	668-669	2
β-strand	670-672	3	20
α-helix	673-683	11
α-helix	688-696	9
β-strand	702-705	4	20
α-helix	708-718	11
α-helix	725-733	9

Chain C: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	21
α-helix	14-17	4
β-strand	22	1	22
β-strand	23	1	21
β-strand	31	1	23
β-strand	33	1	23
β-strand	34-40	7	21
β-strand	43-48	6	21
β-strand	49	1	22
α-helix	56	1
β-strand	59-62	4	21
α-helix	64-67	4
β-strand	77-80	4	21
β-strand	82-83	2	21
β-strand	91-99	9	24
β-strand	101	1	25
β-strand	111-113	3	26
α-helix	115-124	10
β-strand	128-131	4	24
β-strand	135	1	27
β-strand	138-139	2	25
β-strand	144-145	2	25
β-strand	148	1	27
β-strand	149-154	6	24
β-strand	171	1	24
β-strand	174-187	14	24
α-helix	188	1
β-strand	194-196	3	26
α-helix	225-239	15
α-helix	244-248	5
α-helix	251-253	3
β-strand	255-259	5	28
α-helix	266-277	12
β-strand	284-286	3	28
α-helix	298-316	19
β-strand	323-328	6	28
α-helix	330-333	4
α-helix	349-358	10
β-strand	367-373	7	28
α-helix	381-384	4
β-strand	391-394	4	28
α-helix	396	1
α-helix	398-399	2
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	29
α-helix	549-560	12
β-strand	564-568	5	29
α-helix	578-594	17
β-strand	597-602	6	29
α-helix	605-609	5
β-strand	612	1	30
β-strand	617	1	30
α-helix	620-631	12
α-helix	634	1
β-strand	639-646	8	29
α-helix	649-655	7
α-helix	657-660	4
β-strand	663-666	4	29
α-helix	668-669	2
β-strand	670-672	3	31
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	31
α-helix	707-719	13
α-helix	726-736	11

Chain D: 32 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	8-10	3	33
α-helix	15-18	4
β-strand	22-24	3	33
β-strand	31	1	34
β-strand	33	1	34
β-strand	34-40	7	32
β-strand	43-48	6	32
β-strand	49-51	3	33
α-helix	56	1
β-strand	60-62	3	33
α-helix	66-68	3
β-strand	77-83	7	32
β-strand	91-99	9	35
β-strand	101	1	36
β-strand	111-113	3	37
α-helix	114-121	8
β-strand	128-131	4	35
β-strand	135-139	5	36
β-strand	144-148	5	36
β-strand	149-154	6	35
β-strand	171	1	35
β-strand	174-187	14	35
β-strand	194-196	3	37
α-helix	224-239	16
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	38
α-helix	266-277	12
β-strand	284-286	3	38
α-helix	296-316	21
β-strand	323-328	6	38
α-helix	349-356	8
β-strand	367-373	7	38
α-helix	381-384	4
β-strand	391-394	4	38
α-helix	396	1
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	39
α-helix	549-558	10
β-strand	564-568	5	39
α-helix	570-573	4
α-helix	578-594	17
β-strand	597-602	6	39
α-helix	605-609	5
β-strand	612	1	40
β-strand	617	1	40
α-helix	620-631	12
α-helix	634	1
β-strand	639-645	7	39
α-helix	649-655	7
α-helix	658-660	3
β-strand	663-666	4	39
α-helix	668-669	2
β-strand	670-672	3	41
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	41
α-helix	707-717	11
α-helix	726-735	10

Chain E: 28 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	42
β-strand	8-10	3	43
β-strand	22-24	3	43
β-strand	31	1	44
β-strand	33	1	44
β-strand	34-40	7	42
β-strand	43-48	6	42
β-strand	49-51	3	43
β-strand	60-62	3	43
α-helix	64-70	7
β-strand	77-82	6	42
β-strand	91-99	9	45
β-strand	101	1	46
β-strand	112-113	2	47
α-helix	114-122	9
β-strand	128-131	4	45
β-strand	135-139	5	46
β-strand	144-148	5	46
β-strand	149-154	6	45
β-strand	171	1	45
β-strand	174-187	14	45
β-strand	195-196	2	47
α-helix	225-239	15
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-259	5	48
α-helix	266-277	12
β-strand	284-286	3	48
α-helix	298-316	19
β-strand	323-328	6	48
α-helix	349-358	10
β-strand	367-373	7	48
α-helix	381-384	4
β-strand	391-394	4	48
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	49
α-helix	549-560	12
β-strand	564-566	3	49
α-helix	570-573	4
α-helix	578-594	17
β-strand	598-603	6	49
α-helix	605-609	5
β-strand	612	1	50
β-strand	617	1	50
α-helix	620-631	12
α-helix	634-635	2
β-strand	640-646	7	49
α-helix	649-654	6
α-helix	657-660	4
β-strand	663-666	4	49
α-helix	668-669	2
β-strand	670-672	3	51
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	51
α-helix	707-719	13
α-helix	722-736	15

Chain F: 29 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	52
β-strand	8-10	3	53
α-helix	16-18	3
β-strand	22-24	3	53
β-strand	34-40	7	52
β-strand	43-48	6	52
β-strand	49-51	3	53
β-strand	60-62	3	53
α-helix	64-70	7
β-strand	77-82	6	52
β-strand	91-101	11	54
β-strand	111-113	3	55
α-helix	114-124	11
β-strand	128-131	4	54
β-strand	135-139	5	54
β-strand	144-154	11	54
β-strand	171	1	54
β-strand	174-187	14	54
α-helix	188	1
β-strand	194-196	3	55
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	56
α-helix	266-277	12
β-strand	284-286	3	56
α-helix	298-316	19
β-strand	323-328	6	56
α-helix	349-358	10
β-strand	367-373	7	56
α-helix	381-384	4
β-strand	391-394	4	56
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	57
α-helix	549-560	12
β-strand	564-568	5	57
α-helix	578-594	17
β-strand	597-602	6	57
α-helix	605-609	5
β-strand	612	1	58
β-strand	617	1	58
α-helix	620-631	12
α-helix	634-635	2
β-strand	639-646	8	57
α-helix	649-655	7
α-helix	658-660	3
β-strand	665-666	2	57
β-strand	670-672	3	59
α-helix	673-683	11
α-helix	688-698	11
β-strand	702-705	4	59
α-helix	707-717	11
α-helix	724-735	12

Chain G: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	26-28	3
α-helix	37-54	18
α-helix	59-73	15
α-helix	78-93	16
α-helix	100-114	15
α-helix	117-133	17
α-helix	138-154	17
α-helix	158-175	18
α-helix	179-190	12
α-helix	202-211	10
α-helix	220-227	8
α-helix	237-239	3
α-helix	241-251	11
α-helix	259-269	11
α-helix	274-291	18

Chain H: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	26-29	4
α-helix	37-54	18
α-helix	59-73	15
α-helix	78-94	17
α-helix	100-114	15
α-helix	117-133	17
α-helix	138-154	17
α-helix	158-173	16
α-helix	178-193	16
α-helix	201-203	3
α-helix	204-211	8
α-helix	220-227	8
α-helix	237-239	3
α-helix	241-251	11
α-helix	258-269	12
α-helix	274-292	19

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	188	Rattus norvegicus	P60881

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

>3J99_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

>3J99_2 Alpha-soluble NSF attachment protein (chains G, H, I, J)
GSMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNW
SAAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFT
IAAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQY
QKAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDS
RECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Sequence of entity 3 (K), FASTA

>3J99_3 Vesicle-associated membrane protein 2 (chains K)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW

Sequence of entity 4 (L), FASTA

>3J99_4 Syntaxin-1A (chains L)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK

Sequence of entity 5 (M), FASTA

>3J99_5 Synaptosomal-associated protein 25 (chains M)
RADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEK
NLKDLGKFCGLCVCPCNKLKSSDAYKKAWGNNQDGVVASQPARVVDEREQMAISGGFIRR
VTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEAN
QRATKMLG

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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