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

Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form). Determined by X-ray diffraction at 3.6 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 6,328
Mol. weight: 96.35 kDa
Ligands: CA
Released: 12 Aug 2015

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

Secondary structure: helices and β-sheets

5CCH contains 26 α-helices and 38 β-strands across 6 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-88	60

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	192-254	63

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-82	72

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	141-201	61

Chain E: 12 helices, 20 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	191-192	2
β-strand	193-194	2	2
α-helix	195-198	4
β-strand	205-212	8	1
α-helix	216-218	3
β-strand	223-230	8	2
α-helix	236-237	2
β-strand	238-246	9	2
α-helix	247-249	3
β-strand	256-261	6	1
α-helix	262	1
β-strand	263	1	2
α-helix	264-270	7
β-strand	275-283	9	3
β-strand	288-297	10	3
β-strand	303	1	4
β-strand	306	1	4
β-strand	310-318	9	5
β-strand	321-327	7	5
α-helix	328-330	3
β-strand	338-346	9	3
α-helix	349-354	6
β-strand	356-363	8	5
α-helix	369-370	2
β-strand	371-379	9	5
α-helix	384-395	12
β-strand	401-406	6	3
β-strand	408	1	5
α-helix	410-418	9

Chain F: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	144-152	9	6
β-strand	157-166	10	6
α-helix	168-170	3
β-strand	179-185	7	7
α-helix	191-192	2
β-strand	193-194	2	7
α-helix	195-198	4
β-strand	205-212	8	6
α-helix	216-219	4
β-strand	223-230	8	7
α-helix	236-237	2
β-strand	238-246	9	7
α-helix	247-249	3
β-strand	256-261	6	6
β-strand	263	1	7
β-strand	275-283	9	8
β-strand	288-297	10	8
β-strand	310-318	9	9
β-strand	321-327	7	9
α-helix	328-332	5
β-strand	338-346	9	8
α-helix	349-354	6
β-strand	356-363	8	9
β-strand	371-379	9	9
α-helix	384-395	12
β-strand	401-406	6	8
β-strand	408	1	9
α-helix	410-417	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vesicle-associated membrane protein 2	A	protein	63	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	B	protein	67	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	C	protein	77	Rattus norvegicus	P60881 (AlphaFold model)
Synaptosomal-associated protein 25	D	protein	65	Rattus norvegicus	P60881 (AlphaFold model)
Synaptotagmin-1	E, F	protein	281	Rattus norvegicus	P21707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5CCH_1 Vesicle-associated membrane protein 2 (chains A)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW

Sequence of entity 2 (B), FASTA

>5CCH_2 Syntaxin-1A (chains B)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK

Sequence of entity 3 (C), FASTA

>5CCH_3 Synaptosomal-associated protein 25 (chains C)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK

Sequence of entity 4 (D), FASTA

>5CCH_4 Synaptosomal-associated protein 25 (chains D)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG

Sequence of entity 5 (E, F), FASTA

>5CCH_5 Synaptotagmin-1 (chains E, F)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNG
KRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGY
NSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7

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
5CCG 3.5 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form)
7UDB 3.5 Å, Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2
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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