1K5W: Synaptotagmin I

Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine. Determined by solution NMR. Released 23 Jan 2002.

Method: Solution NMR
Organism: Rattus norvegicus
Chains: 1
Atoms: 1,185
Mol. weight: 17.43 kDa
Ligands: CA
Released: 23 Jan 2002

Explore 1K5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K5W contains 3 α-helices and 11 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	275-280	6	1
β-strand	283	1	2
β-strand	288	1	2
β-strand	289-297	9	1
β-strand	310-318	9	3
β-strand	322-327	6	3
β-strand	338-345	8	1
β-strand	355-363	9	3
α-helix	369-370	2
β-strand	371-379	9	3
α-helix	385-395	11
β-strand	401-406	6	1
β-strand	408	1	3
α-helix	410-417	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin I	A	protein	152	Rattus norvegicus	P21707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1K5W_1 Synaptotagmin I (chains A)
QEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTT
IKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRH
WSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine. Fernandez, I., Arac, D., Ubach, J. et al. Neuron (2001) 32:1057-1069. DOI 10.1016/S0896-6273(01)00548-7 · 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
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

Browse structure collections

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