6MDM: Vesicle-fusing ATPase

The 20S supercomplex engaging the SNAP-25 N-terminus (class 1). Determined by electron microscopy at 4.4 Å resolution. Released 19 Sept 2018.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Cricetulus griseus, Rattus norvegicus
Chains: 11
Atoms: 36,567
Mol. weight: 655.8 kDa
Ligands: ADP, ATP
Released: 19 Sept 2018

Explore 6MDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MDM contains 226 α-helices and 173 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: 32 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	8-10	3	2
α-helix	14-17	4
β-strand	22-24	3	2
β-strand	31	1	3
β-strand	33	1	3
β-strand	34-38	5	1
β-strand	44-48	5	1
β-strand	49-51	3	2
α-helix	56	1
β-strand	60-62	3	2
α-helix	64-70	7
β-strand	77-82	6	1
β-strand	91	1	4
β-strand	92-97	6	5
β-strand	100-101	2	6
β-strand	111-113	3	7
α-helix	114-124	11
β-strand	128-131	4	4
β-strand	135-136	2	8
β-strand	139-140	2	9
β-strand	143-144	2	9
β-strand	145-146	2	6
β-strand	147-148	2	8
β-strand	149-154	6	5
β-strand	171	1	5
β-strand	174-177	4	4
β-strand	182-185	4	5
β-strand	194-196	3	7
β-strand	200	1	5
α-helix	224-229	6
α-helix	230-234	5
α-helix	242-248	7
α-helix	250-253	4
β-strand	255-259	5	10
α-helix	267-276	10
β-strand	279-285	7	10
α-helix	297-316	20
α-helix	320-321	2
β-strand	322-327	6	10
β-strand	335	1	11
α-helix	350-359	10
β-strand	367-373	7	10
β-strand	379	1	11
β-strand	391-394	4	10
α-helix	397-399	3
α-helix	400-417	18
α-helix	426-431	6
α-helix	438-455	18
α-helix	482-485	4
α-helix	489-491	3
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	12
α-helix	549-559	11
β-strand	564-568	5	12
α-helix	570-573	4
α-helix	578-593	16
β-strand	597-602	6	12
α-helix	605-608	4
β-strand	612	1	13
β-strand	617	1	13
α-helix	620-631	12
α-helix	633-634	2
β-strand	639-644	6	12
α-helix	650-654	5
β-strand	663-666	4	12
α-helix	668-669	2
β-strand	670	1	14
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	14
α-helix	707-718	12
α-helix	722-733	12

Chain B: 32 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	15
α-helix	16-18	3
β-strand	21-24	4	15
β-strand	34-40	7	15
β-strand	43-51	9	15
α-helix	56	1
β-strand	60-62	3	15
α-helix	64-67	4
β-strand	77-83	7	15
α-helix	87-90	4
β-strand	91	1	16
β-strand	94-100	7	17
β-strand	112-113	2	18
α-helix	114-124	11
β-strand	128-131	4	16
β-strand	135-140	6	17
β-strand	143-153	11	17
β-strand	171-172	2	17
β-strand	174-177	4	16
β-strand	182-187	6	17
β-strand	195-196	2	18
α-helix	224-239	16
α-helix	242-248	7
β-strand	255-259	5	19
α-helix	267-276	10
α-helix	281-282	2
β-strand	283-285	3	19
β-strand	294	1	20
α-helix	297-315	19
α-helix	320-322	3
β-strand	325-327	3	19
α-helix	330-333	4
α-helix	349-358	10
β-strand	369-373	5	19
α-helix	376-378	3
α-helix	381-384	4
β-strand	392-394	3	19
α-helix	400-416	17
α-helix	426-432	7
α-helix	440-454	15
α-helix	482-485	4
α-helix	499-501	3
α-helix	512-529	18
β-strand	539-542	4	21
α-helix	549-559	11
β-strand	564-568	5	21
α-helix	578-592	15
β-strand	597-602	6	21
α-helix	605-608	4
β-strand	612	1	22
β-strand	617	1	22
α-helix	620-629	10
α-helix	634	1
β-strand	639-646	8	21
α-helix	650-655	6
β-strand	663-666	4	21
α-helix	667-669	3
β-strand	670-672	3	23
α-helix	673-683	11
α-helix	689-697	9
β-strand	702-705	4	23
α-helix	707-718	12
α-helix	722-734	13

Chain C: 34 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	8-10	3	25
α-helix	16-18	3
β-strand	22-24	3	25
β-strand	31	1	26
β-strand	33	1	26
β-strand	34-40	7	24
β-strand	43-48	6	24
β-strand	49-51	3	25
β-strand	60-62	3	25
α-helix	64-70	7
β-strand	77-82	6	24
α-helix	87-90	4
β-strand	91	1	27
β-strand	92	1	28
β-strand	94-99	6	29
β-strand	101	1	30
α-helix	104-106	3
β-strand	111-113	3	31
α-helix	114-124	11
β-strand	129-131	3	27
β-strand	135-139	5	30
β-strand	144-148	5	30
β-strand	149-151	3	29
β-strand	152-154	3	28
β-strand	170-172	3	28
β-strand	174-176	3	27
β-strand	182-187	6	29
β-strand	194-196	3	31
α-helix	198-200	3
β-strand	212	1	32
α-helix	224-235	12
α-helix	242-248	7
α-helix	251-253	3
β-strand	257-259	3	33
α-helix	266-272	7
α-helix	273-277	5
β-strand	278	1	32
α-helix	281-282	2
β-strand	283-284	2	34
α-helix	297-316	20
β-strand	323-326	4	34
α-helix	348-358	11
β-strand	367-370	4	34
β-strand	371-373	3	33
α-helix	376-378	3
α-helix	381-384	4
β-strand	392-394	3	33
α-helix	397-399	3
α-helix	400-416	17
α-helix	426-432	7
α-helix	439-456	18
α-helix	481-485	5
α-helix	498-502	5
α-helix	512-530	19
β-strand	536-542	7	35
α-helix	550-560	11
β-strand	564	1	35
β-strand	568	1	36
α-helix	578-592	15
β-strand	597-601	5	35
β-strand	602	1	36
α-helix	605-608	4
β-strand	612	1	37
β-strand	617	1	37
α-helix	620-631	12
α-helix	634	1
β-strand	639-646	8	35
α-helix	650-654	5
β-strand	663-666	4	35
α-helix	667-668	2
α-helix	673-683	11
α-helix	691-698	8
α-helix	707-718	12
α-helix	722-737	16

Chain D: 32 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	38
α-helix	15-18	4
β-strand	21-24	4	38
β-strand	31	1	39
β-strand	33	1	39
β-strand	34-38	5	38
β-strand	44-51	8	38
α-helix	56	1
β-strand	60-62	3	38
α-helix	64-70	7
β-strand	77-82	6	38
β-strand	91	1	40
β-strand	92-100	9	41
β-strand	111-113	3	42
α-helix	114-124	11
β-strand	129-131	3	40
β-strand	135-136	2	41
β-strand	139-140	2	43
β-strand	143-144	2	43
β-strand	146-154	9	41
β-strand	170-171	2	41
β-strand	174-176	3	40
β-strand	182-187	6	41
β-strand	194-196	3	42
α-helix	224-234	11
α-helix	236-239	4
α-helix	243-247	5
α-helix	250-253	4
β-strand	255-259	5	44
α-helix	266-275	10
α-helix	281-282	2
β-strand	283-284	2	44
α-helix	299-315	17
β-strand	323-326	4	44
α-helix	330-333	4
α-helix	346-349	4
α-helix	350-358	9
β-strand	367-373	7	44
α-helix	381-383	3
β-strand	392-394	3	44
α-helix	397-399	3
α-helix	402-416	15
α-helix	426-432	7
α-helix	439-457	19
α-helix	469-471	3
α-helix	482-488	7
α-helix	512-530	19
β-strand	536-542	7	45
α-helix	549-560	12
β-strand	565-568	4	45
α-helix	578-593	16
β-strand	597-602	6	45
α-helix	605-608	4
β-strand	612-613	2	46
β-strand	616-617	2	46
α-helix	620-630	11
α-helix	632-634	3
β-strand	639-646	8	45
α-helix	652-654	3
β-strand	663-666	4	45
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-718	12
α-helix	722-736	15

Chain E: 31 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	217-219	3
α-helix	224-230	7
α-helix	231-235	5
α-helix	251-253	3
β-strand	255	1	47
β-strand	258-259	2	47
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-285	3	47
α-helix	287-290	4
α-helix	297-311	15
α-helix	312-316	5
β-strand	324-328	5	47
α-helix	330-333	4
α-helix	352-355	4
α-helix	356-360	5
β-strand	368-372	5	47
α-helix	377-383	7
β-strand	393-394	2	47
α-helix	395-399	5
α-helix	400-415	16
α-helix	426-432	7
α-helix	439-454	16
α-helix	480-488	9
α-helix	512-530	19
β-strand	539	1	48
β-strand	540-542	3	49
α-helix	550-560	11
β-strand	564-568	5	49
α-helix	570-573	4
α-helix	578-594	17
β-strand	598-602	5	49
α-helix	605-608	4
β-strand	612	1	50
β-strand	617	1	50
α-helix	620-631	12
α-helix	634	1
β-strand	641-646	6	49
α-helix	650-654	5
β-strand	663	1	48
β-strand	666	1	49
α-helix	668-670	3
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-718	12
α-helix	726-733	8

Chain F: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	225-238	14
β-strand	258-259	2	51
α-helix	266-277	12
α-helix	281-283	3
β-strand	285-286	2	51
α-helix	300-315	16
β-strand	324-328	5	51
α-helix	348-358	11
β-strand	368-373	6	51
α-helix	400-406	7
α-helix	407-411	5
α-helix	428-431	4
α-helix	433-435	3
α-helix	444-453	10
α-helix	473-476	4
α-helix	500-502	3
α-helix	512-529	18
β-strand	536-542	7	52
α-helix	550-559	10
β-strand	564-568	5	52
α-helix	578-594	17
β-strand	598-602	5	52
α-helix	605-608	4
β-strand	612	1	53
β-strand	617	1	53
α-helix	620-631	12
α-helix	632-634	3
β-strand	640-646	7	52
α-helix	650-654	5
β-strand	662-666	5	52
α-helix	668-670	3
α-helix	673-683	11
α-helix	688-695	8
α-helix	707-719	13
α-helix	725-735	11

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	20
α-helix	20-23	4
α-helix	24-34	11
α-helix	37-71	35
α-helix	74-82	9
α-helix	143-200	58

Chain I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	192-236	45
α-helix	239-251	13

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	768	Cricetulus griseus	P18708 (AlphaFold model)
Synaptosomal-associated protein 25	H	protein	207	Rattus norvegicus	P60881 (AlphaFold model)
Syntaxin-1A	I	protein	256	Rattus norvegicus	P32851 (AlphaFold model)
Vesicle-associated membrane protein 2	J	protein	117	Rattus norvegicus	P63045 (AlphaFold model)
Alpha-soluble NSF attachment protein	K, L	protein	313	Rattus norvegicus	P54921

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

>6MDM_1 Vesicle-fusing ATPase (chains A, B, C, D, E, F)
MGHHHHHHDYDIPTTENLYFQGAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVI
VRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMT
IEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMD
PSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFE
KMGIGGLDKEFSDIFRRAFASRVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKM
LNAREPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQ
RGSMAGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIG
LPDEKGRLQILHIHTARMRGHQLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRH
IIASTKVEVDMEKAESLQVTRGDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTR
VLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGF
SETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQ
GRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQ
QVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLDFD

Sequence of entity 2 (H), FASTA

>6MDM_2 Synaptosomal-associated protein 25 (chains H)
MASMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQL
DRVEEGMNHINQDMKEAEKNLKDLGKCCGLFICPCNKLKSSDAYKKAWGNNQDGVVASQP
ARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQ
IDRIMEKADSNKTRIDEANQRATKMLG

Sequence of entity 3 (I), FASTA

>6MDM_3 Syntaxin-1A (chains I)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERSKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVK

Sequence of entity 4 (J), FASTA

>6MDM_4 Vesicle-associated membrane protein 2 (chains J)
MASYYHHHHHHDYDIPTSENLYFQGASHMSATAATVPPAAPAGEGGPPAPPPNLTSNRRL
QQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW

Sequence of entity 5 (K, L), FASTA

>6MDM_5 Alpha-soluble NSF attachment protein (chains K, L)
MHHHHHHHHHHENLYFQGMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEAC
EIYARAANMFKMAKNWSAAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAIN
CLMRAIEIYTDMGRFTIAAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSAN
KCLLKVAGYAAQLEQYQKAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAK
LAVQKYEELFPAFSDSRECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLR
IKKTIQGDEEDLR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	9

Primary citation

Structural principles of SNARE complex recognition by the AAA+ protein NSF. White, K.I., Zhao, M., Choi, U.B. et al. Elife (2018) 7. DOI 10.7554/eLife.38888 · 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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