4V11: Synaptotagmin-1

Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84. Determined by X-ray diffraction at 1.95 Å resolution. Released 25 Feb 2015.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 1,443
Mol. weight: 18.46 kDa
Ligands: CA
Released: 25 Feb 2015

Explore 4V11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V11 contains 7 α-helices and 10 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	276-284	9	1
α-helix	285-287	3
β-strand	289-298	10	1
α-helix	300-302	3
β-strand	311-319	9	2
β-strand	322-328	7	2
α-helix	329-333	5
β-strand	339-347	9	1
α-helix	350-352	3
β-strand	357-364	8	2
β-strand	373-380	8	2
α-helix	385-396	12
β-strand	402-407	6	1
β-strand	409	1	2
α-helix	411-417	7

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	82-84	3
β-strand	85	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A	protein	150	HOMO SAPIENS	P21579 (AlphaFold model)
Synaptic vesicle glycoprotein 2A	B	protein	10	HOMO SAPIENS	Q7L0J3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4V11_1 SYNAPTOTAGMIN-1 (chains A)
KLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIK
KNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWS
DMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Sequence of entity 2 (B), FASTA

>4V11_2 SYNAPTIC VESICLE GLYCOPROTEIN 2A (chains B)
SDATEGHDED

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

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

Primary citation

Phosphorylation of Synaptic Vesicle Protein 2A at Thr84 by Casein Kinase 1 Family Kinases Controls the Specific Retrieval of Synaptotagmin-1. Zhang, N., Gordon, S.L., Fritsch, M.J. et al. J Neurosci (2015) 35:2492. DOI 10.1523/JNEUROSCI.4248-14.2015 · PubMed

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)
3F05 1.4 Å, Crystal Structure of Synaptotagmin I C2A domain with Mn(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)
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…

Browse structure collections

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