7U4Q: Human Synaptotagmin-1 C2A Y181F Ca2+ bound

Human Synaptotagmin-1 C2A Y181F Ca2+ bound. Determined by X-ray diffraction at 1.56 Å resolution. Released 15 Mar 2023.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,388
Mol. weight: 30.71 kDa
Ligands: CA
Released: 15 Mar 2023

Explore 7U4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U4Q contains 8 α-helices and 20 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	145-153	9	1
β-strand	158-167	10	1
β-strand	173	1	2
β-strand	177	1	2
β-strand	180-187	8	3
β-strand	193-195	3	3
α-helix	196-200	5
β-strand	206-214	9	1
α-helix	217-220	4
β-strand	224-231	8	3
α-helix	237-238	2
β-strand	239-247	9	3
α-helix	248-250	3
β-strand	258-262	5	1
β-strand	264	1	3

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	145-153	9	4
β-strand	158-167	10	4
β-strand	180-187	8	5
β-strand	189-195	7	5
α-helix	196-200	5
β-strand	206-214	9	4
α-helix	217-219	3
β-strand	224-231	8	5
α-helix	238	1
β-strand	239-247	9	5
α-helix	248-250	3
β-strand	258-262	5	4
β-strand	264	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A, B	protein	133	Homo sapiens	P21579 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7U4Q_1 Synaptotagmin-1 (chains A, B)
GDITHMEKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPFVKVFLLPDKKKKF
ETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFG
HVTEEWRDLQSAE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability. Dominguez, M.J., Bui, A.A., Villarreal, J. et al. Biophys J (2024). DOI 10.1016/j.bpj.2024.11.009 · 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)
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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