2YOA: Synaptotagmin-1 C2B domain with phosphoserine

Synaptotagmin-1 C2B domain with phosphoserine. Determined by X-ray diffraction at 1.5 Å resolution. Released 20 Mar 2013.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: RATTUS NORVEGICUS
Chains: 2
Atoms: 2,713
Mol. weight: 35.65 kDa
Ligands: SCN, SEP, CA
Released: 20 Mar 2013

Explore 2YOA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YOA contains 12 α-helices and 18 β-strands across 2 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	275-283	9	1
α-helix	284-286	3
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	349-352	4
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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	275-283	9	3
α-helix	284-286	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	328-330	3
β-strand	338-346	9	3
α-helix	349-354	6
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	410-417	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A, B	protein	152	RATTUS NORVEGICUS	P21707 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2YOA_1 SYNAPTOTAGMIN-1 (chains A, B)
MEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTT
IKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRH
WSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	5
SEP	Phosphoserine	C3 H8 N O6 P	2
CA	Calcium ion	Ca	7

Primary citation

Phosphatidylinositol 4,5-Bisphosphate Clusters Act as Molecular Beacons for Vesicle Recruitment. Honigmann, A., Van Den Bogaart, G., Iraheta, E. et al. Nat Struct Mol Biol (2013) 20:679. DOI 10.1038/NSMB.2570 · 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
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

About this viewer

MolViewer shows 2YOA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.