1TJM: Synaptotagmin I

Crystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain. Determined by X-ray diffraction at 1.18 Å resolution. Released 28 Sept 2004.

Method: X-ray diffraction
Resolution: 1.18 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 1,463
Mol. weight: 18 kDa
Ligands: SR
Released: 28 Sept 2004

Explore 1TJM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TJM contains 7 α-helices and 9 β-strands across 1 chain. 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	269-271	3
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	328-330	3
β-strand	338-346	9	1
α-helix	352-354	3
β-strand	356-363	8	2
α-helix	369-371	3
β-strand	372-379	8	2
α-helix	384-395	12
β-strand	401-406	6	1
β-strand	408	1	2
α-helix	410-417	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin I	A	protein	159	Rattus norvegicus	P21707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1TJM_1 Synaptotagmin I (chains A)
SGGGGGILEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKR
LKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNS
TGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Ligands and cofactors

ID	Name	Formula	Copies
SR	Strontium ion	Sr	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain. Cheng, Y., Sequeira, S.M., Malinina, L. et al. Protein Sci (2004) 13:2665-2672. DOI 10.1110/ps.04832604 · 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
2YOA 1.5 Å, Synaptotagmin-1 C2B domain with phosphoserine
1UOV 1.65 Å, Calcium binding domain C2B
5CCJ 1.65 Å, Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain
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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