9PBF: Syntaxin-1A

21bin20S complex (NSF-alphaSNAP-2:1 syntaxin-1a:SNAP-25), non-hydrolyzing, class 10. Determined by electron microscopy at 4.01 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 4.01 Å
Organisms: Rattus norvegicus, Cricetulus griseus
Chains: 12
Atoms: 43,439
Mol. weight: 689.94 kDa
Ligands: ADP, ATP
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9PBF contains 257 α-helices and 189 β-strands across 12 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: 35 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	21
α-helix	14-19	6
β-strand	21-24	4	21
β-strand	34-37	4	21
β-strand	45-51	7	21
α-helix	56	1
β-strand	59-62	4	21
α-helix	64-70	7
β-strand	77-83	7	21
α-helix	87-90	4
β-strand	91	1	22
β-strand	94-99	6	23
β-strand	101	1	23
α-helix	104-106	3
β-strand	111-113	3	24
α-helix	114-124	11
β-strand	129-131	3	22
β-strand	135-139	5	23
β-strand	144-152	9	23
β-strand	172	1	23
β-strand	174-176	3	22
β-strand	182-187	6	23
α-helix	188	1
β-strand	194-196	3	24
α-helix	228-234	7
α-helix	242-247	6
β-strand	255-259	5	25
α-helix	266-275	10
β-strand	283-286	4	25
α-helix	287-290	4
α-helix	297-304	8
α-helix	307-315	9
β-strand	325-328	4	25
α-helix	330-332	3
α-helix	348-358	11
β-strand	369-373	5	25
α-helix	382-384	3
β-strand	391-394	4	25
α-helix	400-416	17
α-helix	426-431	6
α-helix	438-462	25
α-helix	467-472	6
α-helix	477-486	10
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	26
α-helix	549-559	11
β-strand	564-568	5	26
α-helix	570-572	3
α-helix	578-593	16
β-strand	597-602	6	26
α-helix	605-609	5
α-helix	620-628	9
α-helix	632-634	3
β-strand	639-645	7	26
α-helix	649-654	6
α-helix	657-659	3
β-strand	665-666	2	26
β-strand	670	1	27
α-helix	673-683	11
α-helix	688-697	10
β-strand	705	1	27
α-helix	707-717	11
α-helix	725-735	11

Chain B: 36 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	28
α-helix	14-19	6
β-strand	22-24	3	28
β-strand	34-40	7	28
β-strand	43-51	9	28
α-helix	56	1
β-strand	59-62	4	28
α-helix	64-70	7
β-strand	77-83	7	28
α-helix	87-90	4
β-strand	91	1	29
β-strand	94-100	7	30
β-strand	111-112	2	31
α-helix	114-125	12
β-strand	129-131	3	29
β-strand	135-140	6	30
β-strand	143-152	10	30
β-strand	174-176	3	29
β-strand	182-187	6	30
β-strand	194-195	2	31
α-helix	201-202	2
β-strand	209	1	32
α-helix	216-218	3
α-helix	224-234	11
α-helix	236-239	4
α-helix	242-248	7
α-helix	251-253	3
β-strand	255-259	5	33
α-helix	266-276	11
β-strand	277	1	32
α-helix	281-282	2
β-strand	283-285	3	33
α-helix	298-305	8
α-helix	307-315	9
β-strand	325-327	3	33
α-helix	330-332	3
α-helix	345-358	14
β-strand	369-373	5	33
α-helix	382-384	3
β-strand	392-394	3	33
α-helix	400-410	11
α-helix	413-416	4
β-strand	420	1	34
α-helix	426-432	7
α-helix	438-458	21
β-strand	475	1	34
α-helix	477-486	10
α-helix	497-502	6
α-helix	512-530	19
β-strand	538-542	5	35
α-helix	550-559	10
β-strand	565-568	4	35
α-helix	570-573	4
α-helix	578-593	16
β-strand	599-602	4	35
α-helix	605-609	5
α-helix	620-629	10
β-strand	642-646	5	35
α-helix	649-655	7
α-helix	658-660	3
β-strand	663-666	4	35
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	725-736	12

Chain C: 31 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	8-10	3	2
α-helix	14-19	6
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	64-70	7
β-strand	77-82	6	1
α-helix	87-90	4
β-strand	91	1	3
β-strand	95-101	7	4
α-helix	104-106	3
β-strand	111-112	2	5
α-helix	114-124	11
β-strand	128-131	4	3
β-strand	135-140	6	4
β-strand	143-152	10	4
β-strand	174-177	4	3
β-strand	183-187	5	4
β-strand	194-195	2	5
β-strand	209	1	6
α-helix	215-218	4
α-helix	224-239	16
α-helix	244-248	5
β-strand	256-259	4	7
α-helix	266-276	11
β-strand	277	1	6
α-helix	281-282	2
β-strand	283-286	4	7
α-helix	297-316	20
β-strand	325-328	4	7
β-strand	335	1	8
α-helix	346-358	13
β-strand	369-373	5	7
β-strand	379	1	8
α-helix	382-384	3
β-strand	391-394	4	7
α-helix	400-416	17
β-strand	420	1	9
α-helix	427-432	6
α-helix	438-454	17
α-helix	467-470	4
β-strand	475	1	9
α-helix	477-486	10
α-helix	496-502	7
α-helix	512-529	18
β-strand	536-542	7	10
α-helix	549-558	10
β-strand	564-568	5	10
α-helix	578-592	15
β-strand	597-602	6	10
α-helix	605-609	5
β-strand	612	1	11
β-strand	617	1	11
α-helix	620-629	10
β-strand	639-646	8	10
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	10
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-718	12
α-helix	725-736	12

Chain D: 34 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	37
α-helix	14-18	5
β-strand	22-24	3	37
β-strand	34-40	7	37
β-strand	43-51	9	37
α-helix	56	1
β-strand	59-62	4	37
α-helix	64-69	6
β-strand	77-82	6	37
α-helix	87-90	4
β-strand	91	1	38
β-strand	94-101	8	39
α-helix	104-106	3
β-strand	112-113	2	40
α-helix	114-124	11
β-strand	129-131	3	38
β-strand	135-140	6	39
β-strand	143-152	10	39
β-strand	174-176	3	38
β-strand	182-187	6	39
β-strand	195-196	2	40
β-strand	209	1	41
α-helix	224-239	16
α-helix	242-248	7
β-strand	256-259	4	42
α-helix	266-276	11
β-strand	277	1	41
α-helix	281-282	2
β-strand	283-284	2	42
α-helix	297-304	8
α-helix	307-316	10
β-strand	323-326	4	42
α-helix	347-358	12
β-strand	367-373	7	42
α-helix	376-378	3
α-helix	381-383	3
β-strand	391-394	4	42
α-helix	400-416	17
β-strand	420	1	43
α-helix	426-432	7
α-helix	438-453	16
β-strand	457	1	44
β-strand	465	1	44
β-strand	475	1	43
α-helix	477-486	10
α-helix	496-502	7
α-helix	513-530	18
β-strand	536-542	7	45
α-helix	549-559	11
β-strand	564-568	5	45
α-helix	570-573	4
α-helix	578-594	17
β-strand	597-602	6	45
α-helix	605-608	4
α-helix	620-629	10
α-helix	632-635	4
β-strand	639-645	7	45
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	45
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-717	11
α-helix	722-724	3
α-helix	726-736	11

Chain E: 36 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	46
α-helix	14-19	6
α-helix	21	1
β-strand	22-24	3	46
β-strand	34-40	7	46
β-strand	43-51	9	46
α-helix	56	1
β-strand	59-62	4	46
α-helix	64-70	7
β-strand	77-83	7	46
α-helix	87-90	4
β-strand	91	1	47
β-strand	94-101	8	48
α-helix	104-106	3
β-strand	112-113	2	49
α-helix	114-124	11
β-strand	128-131	4	47
β-strand	135-140	6	48
β-strand	143-152	10	48
β-strand	174-177	4	47
β-strand	182-187	6	48
α-helix	188	1
β-strand	195-196	2	49
β-strand	200	1	48
α-helix	224-230	7
α-helix	231-235	5
α-helix	236-239	4
α-helix	242-248	7
β-strand	256-257	2	50
α-helix	266-276	11
α-helix	281-282	2
β-strand	283-285	3	50
α-helix	297-316	20
α-helix	317-319	3
β-strand	323-328	6	50
α-helix	330-333	4
α-helix	346-358	13
β-strand	367-372	6	50
α-helix	376-378	3
β-strand	391-392	2	50
α-helix	400-416	17
α-helix	426-432	7
α-helix	438-454	17
β-strand	458	1	51
β-strand	464	1	51
α-helix	477-486	10
α-helix	493-494	2
α-helix	499-502	4
α-helix	512-529	18
β-strand	536-542	7	52
α-helix	549-559	11
β-strand	564-568	5	52
α-helix	578-594	17
β-strand	598-603	6	52
β-strand	612	1	53
β-strand	617	1	53
α-helix	620-629	10
β-strand	640-646	7	52
α-helix	649-654	6
α-helix	658-660	3
β-strand	663-666	4	52
β-strand	670-672	3	54
α-helix	673-683	11
α-helix	688-697	10
β-strand	702-705	4	54
α-helix	707-717	11
α-helix	722-724	3
α-helix	725-737	13

Chain F: 33 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
α-helix	14-19	6
β-strand	21-24	4	12
β-strand	34-40	7	12
β-strand	43-51	9	12
α-helix	56	1
β-strand	59-61	3	12
α-helix	64-70	7
β-strand	77-82	6	12
α-helix	87-90	4
β-strand	91	1	13
β-strand	94-101	8	14
α-helix	104-106	3
β-strand	111-113	3	15
α-helix	114-125	12
β-strand	129-131	3	13
β-strand	135-139	5	14
β-strand	144-152	9	14
β-strand	174-176	3	13
β-strand	182-187	6	14
α-helix	188	1
β-strand	194-196	3	15
α-helix	224-233	10
α-helix	235-237	3
α-helix	242-248	7
β-strand	255-259	5	16
α-helix	266-276	11
β-strand	279	1	17
α-helix	281-282	2
β-strand	283	1	16
α-helix	297-316	20
β-strand	322	1	17
β-strand	323-328	6	16
α-helix	330-333	4
α-helix	345-358	14
β-strand	367-372	6	16
α-helix	376-378	3
α-helix	381-384	4
β-strand	391-394	4	16
α-helix	400-416	17
β-strand	420	1	18
α-helix	426-432	7
α-helix	438-455	18
β-strand	475	1	18
α-helix	477-485	9
α-helix	500-502	3
α-helix	513-529	17
β-strand	536-542	7	19
α-helix	550-560	11
β-strand	564-568	5	19
α-helix	570-572	3
α-helix	578-594	17
β-strand	597-603	7	19
α-helix	605-608	4
β-strand	611-612	2	20
β-strand	617-618	2	20
α-helix	620-629	10
β-strand	639-645	7	19
α-helix	649-655	7
β-strand	663-666	4	19
α-helix	673-683	11
α-helix	688-698	11
α-helix	707-717	11
α-helix	725-736	12

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	191-198	8
α-helix	201-258	58

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-81	76
α-helix	141-201	61

4 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
Syntaxin-1A	G, I	protein	267	Rattus norvegicus	P32851 (AlphaFold model)
Alpha-soluble NSF attachment protein	J, K, L	protein	296	Rattus norvegicus	P54921 (AlphaFold model)
Vesicle-fusing ATPase	A, B, C, D, E, F	protein	747	Cricetulus griseus	P18708 (AlphaFold model)
Synaptosomal-associated protein 25	H	protein	222	Rattus norvegicus	P60881 (AlphaFold model)

Sequence of entity 1 (G, I), FASTA

>9PBF_1 Syntaxin-1A (chains G, I)
MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSA
ILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQH
STLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASG
IIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHA
VDYVERAVSDTKKAVKYQSKARRKKIM

Sequence of entity 2 (J, K, L), FASTA

>9PBF_2 Alpha-soluble NSF attachment protein (chains J, K, L)
GMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWS
AAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTI
AAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQ
KAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSR
ECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Sequence of entity 3 (A, B, C, D, E, F), FASTA

>9PBF_3 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 4 (H), FASTA

>9PBF_4 Synaptosomal-associated protein 25 (chains H)
MGSSHHHHHHSQDPNSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGI
RTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLGKFAGLAVAPANKLKSSDAYKKA
WGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMA
LDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLGSG

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 P32851 (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
1EZ3 1.9 Å, Crystal structure of the neuronal T-snare syntaxin-1A
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
3RK2 2.2 Å, Truncated SNARE complex
1KIL 2.3 Å, Three-dimensional structure of the complexin/SNARE complex
1HVV 2.4 Å, Self-association of the H3 region of syntaxin 1A: implications for snare complex assembly
1SFC 2.4 Å, Neuronal synaptic fusion complex
5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
4JEH 2.5 Å, Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex

Browse structure collections

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