3F05: Synaptotagmin I C2A domain with Mn(II)

Crystal Structure of Synaptotagmin I C2A domain with Mn(II). Determined by X-ray diffraction at 1.4 Å resolution. Released 6 Oct 2009.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,419
Mol. weight: 16.09 kDa
Ligands: MN
Released: 6 Oct 2009

Explore 3F05 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F05 contains 10 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	17-140	2
β-strand	144-152	9	1
β-strand	157-166	10	1
α-helix	168-170	3
β-strand	179-186	8	2
α-helix	191-192	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	236-237	2
β-strand	238-246	9	2
α-helix	247-249	3
β-strand	256-261	6	1
α-helix	262	1
β-strand	263	1	2
α-helix	264	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A	protein	143	Homo sapiens	P21579 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3F05_1 Synaptotagmin-1 (chains A)
GSPGIGGGGGGILDSMVEKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVK
VFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGE
FKVPMNTVDFGHVTEEWRDLQSA

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Cystal structure of synaptotagmin I C2A. Guo, F., Dakshinamurthy, R., Thallapuranam, S.K.K. et al. To be published.

Other PDB entries of the same protein (UniProt P21579 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TZ3 1.17 Å, Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+
6U4U 1.3 Å, 1.3 A structure of a pathogenic human Syt 1 C2B (I368T)
3F04 1.35 Å, Crystal Structure of Synaptotagmin I C2A domain
7TUA 1.35 Å, Human Synaptotagmin-1 C2B Y312F without Ca2+
3F00 1.36 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
6U4W 1.4 Å, 1.4 A structure of a pathogenic human Syt 1 C2B (D366E)
7U4Q 1.56 Å, Human Synaptotagmin-1 C2A Y181F Ca2+ bound
3F01 1.7 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
6U41 1.7 Å, 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G)
4V11 1.95 Å, Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
6G5K 2.0 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with…
6QNS 2.4 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant…

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