6MTI: Synaptotagmin-1

Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+. Determined by electron microscopy at 10.4 Å resolution. Released 24 Apr 2019.

Method: Electron microscopy
Resolution: 10.4 Å
Organism: Rattus norvegicus
Chains: 30
Atoms: 23,540
Mol. weight: 347.96 kDa
Ligands: MG
Released: 24 Apr 2019

Explore 6MTI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MTI contains 64 α-helices and 98 β-strands across 30 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.

Chains 1 and 6: 4 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	179-185	7	2
β-strand	193-194	2	2
α-helix	195-199	5
β-strand	205-212	8	1
α-helix	216-219	4
β-strand	223-230	8	2
β-strand	239-246	8	2
β-strand	256-261	6	1
β-strand	263	1	2
α-helix	264-266	3

Chains 2, 3, 4 and 5: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	144-152	9	3
β-strand	157-166	10	3
α-helix	168-170	3
β-strand	179-185	7	4
β-strand	193-194	2	4
α-helix	195-199	5
β-strand	205-212	8	3
α-helix	216-219	4
β-strand	223-230	8	4
β-strand	239-246	8	4
β-strand	256-261	6	3
β-strand	263	1	4
α-helix	264-266	3
β-strand	556-564	9	5
β-strand	569-578	10	5
α-helix	580-582	3
β-strand	589	1	6
β-strand	591-599	9	7
β-strand	602-608	7	7
β-strand	615	1	6
β-strand	619-627	9	5
α-helix	633-635	3
β-strand	637-644	8	7
β-strand	653-660	8	7
α-helix	666-676	11
β-strand	682-687	6	5
β-strand	689	1	7
α-helix	691-698	8

Chains A, E, I, M, Q and U: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-88	60

Chains B, F, J, N, R and V: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	192-255	64

Chains C, G, K, O, S and W: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-81	71

Chains D, H, L, P, T and X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	141-201	61

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	1, 6	protein	127	Rattus norvegicus	P21707 (AlphaFold model)
Synaptotagmin-1	2, 3, 4, 5	protein	281	Rattus norvegicus	P21707 (AlphaFold model)
Vesicle-associated membrane protein 2	A, E, I, M, Q, U	protein	63	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	B, F, J, N, R, V	protein	67	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	C, G, K, O, S, W	protein	77	Rattus norvegicus	P60881 (AlphaFold model)
Synaptosomal-associated protein 25	D, H, L, P, T, X	protein	65	Rattus norvegicus	P60881 (AlphaFold model)

Sequence of entity 1 (1, 6), FASTA

>6MTI_1 Synaptotagmin-1 (chains 1, 6)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEK

Sequence of entity 2 (2, 3, 4, 5), FASTA

>6MTI_2 Synaptotagmin-1 (chains 2, 3, 4, 5)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNG
KRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGY
NSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

Sequence of entity 3 (A, E, I, M, Q, U), FASTA

>6MTI_3 Vesicle-associated membrane protein 2 (chains A, E, I, M, Q, U)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW

Sequence of entity 4 (B, F, J, N, R, V), FASTA

>6MTI_4 Syntaxin-1A (chains B, F, J, N, R, V)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK

Sequence of entity 5 (C, G, K, O, S, W), FASTA

>6MTI_5 Synaptosomal-associated protein 25 (chains C, G, K, O, S, W)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK

Sequence of entity 6 (D, H, L, P, T, X), FASTA

>6MTI_6 Synaptosomal-associated protein 25 (chains D, H, L, P, T, X)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	10

Primary citation

Structural basis for the clamping and Ca2+activation of SNARE-mediated fusion by synaptotagmin. Grushin, K., Wang, J., Coleman, J. et al. Nat Commun (2019) 10:2413-2413. DOI 10.1038/s41467-019-10391-x · 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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