5CCJ: Synaptotagmin-1

Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain. Determined by X-ray diffraction at 1.65 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 6,054
Mol. weight: 72.67 kDa
Released: 12 Aug 2015

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

Secondary structure: helices and β-sheets

5CCJ contains 20 α-helices and 36 β-strands across 4 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: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	275-283	9	1
β-strand	288-297	10	1
α-helix	299-301	3
β-strand	310-318	9	2
β-strand	321-327	7	2
α-helix	328-331	4
β-strand	338-346	9	1
α-helix	349-354	6
β-strand	355-363	9	2
β-strand	371-379	9	2
α-helix	384-395	12
β-strand	401-406	6	1
β-strand	408	1	2
α-helix	410-417	8

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
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
α-helix	328-332	5
β-strand	338-346	9	3
α-helix	349-351	3
β-strand	355-363	9	4
β-strand	371-379	9	4
α-helix	384-395	12
β-strand	401-406	6	3
β-strand	408	1	4
α-helix	410-418	9

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	275-283	9	5
β-strand	288-297	10	5
β-strand	310-318	9	6
β-strand	321-327	7	6
α-helix	328-332	5
β-strand	338-346	9	5
α-helix	349-354	6
β-strand	355-363	9	6
α-helix	370	1
β-strand	371-379	9	6
α-helix	384-395	12
β-strand	401-406	6	5
β-strand	408	1	6
α-helix	410-417	8

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	275-283	9	7
β-strand	288-297	10	7
β-strand	310-318	9	8
β-strand	321-327	7	8
α-helix	328-331	4
β-strand	338-346	9	7
α-helix	349-351	3
β-strand	355-363	9	8
α-helix	369-370	2
β-strand	371-379	9	8
α-helix	384-395	12
β-strand	401-406	6	7
β-strand	408	1	8
α-helix	410-417	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A, B, C, D	protein	152	Rattus norvegicus	P21707 (AlphaFold model)

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

>5CCJ_1 Synaptotagmin-1 (chains A, B, C, D)
SEKLGDICFSLAYVPTAGKLTVVILAAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTT
IKKNTLNPWYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRH
WSDMLANPAAPIAQWHTLQVEEEVDAMLAVKK

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 P21707 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WEE 0.89 Å, High-resolution structure of Synaptotagmin 1 C2A
1TJX 1.04 Å, Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain
1UOW 1.04 Å, Calcium binding domain C2B
1TJM 1.18 Å, Crystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain
2YOA 1.5 Å, Synaptotagmin-1 C2B domain with phosphoserine
1UOV 1.65 Å, Calcium binding domain C2B
8C5H 1.68 Å, NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of…
6CXW 1.83 Å, Synaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function
5W5C 1.85 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex
1RSY 1.9 Å, Structure of the first C2-domain of synaptotagmin I: a novel CA2+(SLASH)PHOSPHOLIPID…
5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
5CCG 3.5 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form)

Browse structure collections

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