5CCG: Ca2+-bound synaptotagmin-1 SNARE complex

Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form). Determined by X-ray diffraction at 3.5 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Rattus norvegicus
Chains: 11
Atoms: 10,575
Mol. weight: 160.64 kDa
Ligands: CA
Released: 12 Aug 2015

Explore 5CCG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CCG contains 31 α-helices and 55 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.

Chains A and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-88	61

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	192-252	61

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-81	71

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	142-201	60

Chain E: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	144-152	9	1
β-strand	157-166	10	1
β-strand	179-185	7	2
α-helix	190-192	3
β-strand	193-194	2	2
β-strand	205-213	9	1
α-helix	219-221	3
β-strand	223-230	8	2
β-strand	239-246	8	2
α-helix	247-249	3
β-strand	256-261	6	1
β-strand	263	1	2
α-helix	264-266	3
β-strand	275-283	9	3
β-strand	288-297	10	3
α-helix	299-301	3
β-strand	310-318	9	4
β-strand	321-327	7	4
β-strand	338-346	9	3
α-helix	352-354	3
β-strand	356-363	8	4
β-strand	372-379	8	4
α-helix	385-395	11
β-strand	397	1	3
β-strand	400-406	7	3
β-strand	408	1	4
α-helix	410-416	7

Chain F: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	144-152	9	5
β-strand	157-166	10	5
β-strand	179-185	7	6
α-helix	191-192	2
β-strand	193-194	2	6
α-helix	195-197	3
β-strand	205-212	8	5
α-helix	219-221	3
β-strand	223-230	8	6
β-strand	239-246	8	6
α-helix	247-249	3
β-strand	256-261	6	5
β-strand	263	1	6
β-strand	275-283	9	7
β-strand	288-297	10	7
α-helix	299-301	3
β-strand	310-318	9	8
β-strand	321-327	7	8
β-strand	338-346	9	7
α-helix	352-354	3
β-strand	356-363	8	8
β-strand	372-379	8	8
α-helix	385-395	11
β-strand	401-406	6	7
β-strand	408	1	8
α-helix	410-416	7

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	192-253	62

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-82	72

2 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-associated membrane protein 2	A, G	protein	63	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	B, H	protein	67	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	C, I	protein	77	Rattus norvegicus	P60881 (AlphaFold model)
Synaptosomal-associated protein 25	D, J	protein	65	Rattus norvegicus	P60881 (AlphaFold model)
Synaptotagmin-1	E, F, K	protein	281	Rattus norvegicus	P21707 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>5CCG_1 Vesicle-associated membrane protein 2 (chains A, G)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW

Sequence of entity 2 (B, H), FASTA

>5CCG_2 Syntaxin-1A (chains B, H)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK

Sequence of entity 3 (C, I), FASTA

>5CCG_3 Synaptosomal-associated protein 25 (chains C, I)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK

Sequence of entity 4 (D, J), FASTA

>5CCG_4 Synaptosomal-associated protein 25 (chains D, J)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG

Sequence of entity 5 (E, F, K), FASTA

>5CCG_5 Synaptotagmin-1 (chains E, F, K)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNG
KRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGY
NSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	19

Primary citation

Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Zhou, Q., Lai, Y., Bacaj, T. et al. Nature (2015) 525:62-67. DOI 10.1038/nature14975 · PubMed

Other PDB entries of the same protein (UniProt P63045 (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
6WVW 2.11 Å, Crystal structure of the R59P-SNAP25 containing SNARE complex
1KIL 2.3 Å, Three-dimensional structure of the complexin/SNARE complex
1SFC 2.4 Å, Neuronal synaptic fusion complex
5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
6A30 2.79 Å, Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region
3HD7 3.4 Å, Helical extension of the neuronal snare complex into the membrane, spacegroup C 1 2 1
7UDB 3.5 Å, Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2
5CCH 3.6 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
6IP1 3.9 Å, alpha-SNAP-SNARE subcomplex in the whole 20S complex
5CCI 4.1 Å, Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form)

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