1BYN: Calcium-bound first C2-domain of synaptotagmin I

Solution structure of the calcium-bound first C2-domain of synaptotagmin I. Determined by solution NMR. Released 21 Oct 1998.

Method: Solution NMR
Organism: Rattus norvegicus
Chains: 1
Atoms: 1,046
Mol. weight: 14.9 kDa
Ligands: CA
Released: 21 Oct 1998

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

Secondary structure: helices and β-sheets

1BYN 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
β-strand	144-152	9	1
β-strand	157-166	10	1
α-helix	168-170	3
β-strand	179-186	8	2
β-strand	193-194	2	2
α-helix	195-197	3
β-strand	205-212	8	1
α-helix	216-219	4
β-strand	223-230	8	2
α-helix	236-238	3
β-strand	239-246	8	2
α-helix	247-249	3
β-strand	255-261	7	1
α-helix	262	1
β-strand	263	1	2
α-helix	264-265	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (synaptotagmin I)	A	protein	128	Rattus norvegicus	P21707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1BYN_1 PROTEIN (SYNAPTOTAGMIN I) (chains A)
EKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHR
KTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEW
RDLQSAEK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

Solution structures of the Ca2+-free and Ca2+-bound C2A domain of synaptotagmin I: does Ca2+ induce a conformational change? Shao, X., Fernandez, I., Sudhof, T.C. et al. Biochemistry (1998) 37:16106-16115. DOI 10.1021/bi981789h · 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

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