5KJ7: Vesicle-associated membrane protein 3
Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction. Determined by X-ray diffraction at 3.5 Å resolution. Released 19 Oct 2016.
- Method
- X-ray diffraction
- Resolution
- 3.5 Å
- Organism
- Rattus norvegicus
- Chains
- 11
- Atoms
- 10,578
- Mol. weight
- 158.77 kDa
- Ligands
- CA
- Released
- 19 Oct 2016
Explore 5KJ7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5KJ7 contains 33 α-helices and 55 β-strands across 11 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 A and G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-88 | 61 | |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 192-254 | 63 | |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-81 | 71 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 142-201 | 60 | |
Chain E: 8 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 144-152 | 9 | 1 |
| β-strand | 157-166 | 10 | 1 |
| β-strand | 179-185 | 7 | 2 |
| α-helix | 190-192 | 3 | |
| β-strand | 193-194 | 2 | 2 |
| β-strand | 205-213 | 9 | 1 |
| α-helix | 218-221 | 4 | |
| β-strand | 223-230 | 8 | 2 |
| β-strand | 239-246 | 8 | 2 |
| α-helix | 247-249 | 3 | |
| β-strand | 256-261 | 6 | 1 |
| β-strand | 263 | 1 | 2 |
| α-helix | 264-266 | 3 | |
| β-strand | 275-283 | 9 | 3 |
| β-strand | 288-297 | 10 | 3 |
| α-helix | 299-301 | 3 | |
| β-strand | 310-318 | 9 | 4 |
| β-strand | 321-327 | 7 | 4 |
| β-strand | 338-346 | 9 | 3 |
| α-helix | 352-354 | 3 | |
| β-strand | 356-363 | 8 | 4 |
| β-strand | 372-379 | 8 | 4 |
| α-helix | 385-395 | 11 | |
| β-strand | 397 | 1 | 3 |
| β-strand | 400-406 | 7 | 3 |
| β-strand | 408 | 1 | 4 |
| α-helix | 410-416 | 7 | |
Chain F: 9 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 144-152 | 9 | 5 |
| β-strand | 157-166 | 10 | 5 |
| β-strand | 179-185 | 7 | 6 |
| α-helix | 191-192 | 2 | |
| β-strand | 193-194 | 2 | 6 |
| α-helix | 195-197 | 3 | |
| β-strand | 205-212 | 8 | 5 |
| α-helix | 219-221 | 3 | |
| β-strand | 223-230 | 8 | 6 |
| β-strand | 239-246 | 8 | 6 |
| α-helix | 247-249 | 3 | |
| β-strand | 256-261 | 6 | 5 |
| β-strand | 263 | 1 | 6 |
| β-strand | 275-283 | 9 | 7 |
| β-strand | 288-297 | 10 | 7 |
| α-helix | 299-301 | 3 | |
| β-strand | 310-318 | 9 | 8 |
| β-strand | 321-327 | 7 | 8 |
| β-strand | 338-346 | 9 | 7 |
| α-helix | 352-354 | 3 | |
| β-strand | 356-363 | 8 | 8 |
| α-helix | 370-371 | 2 | |
| β-strand | 372-379 | 8 | 8 |
| α-helix | 385-395 | 11 | |
| β-strand | 401-406 | 6 | 7 |
| β-strand | 408 | 1 | 8 |
| α-helix | 410-416 | 7 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 192-253 | 62 | |
Chain I: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-82 | 71 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vesicle-associated membrane protein 3 | A, G | protein | 63 | Rattus norvegicus | P63025 (AlphaFold model) |
| Syntaxin-1A | B, H | protein | 66 | Rattus norvegicus | P32851 (AlphaFold model) |
| Synaptosomal-associated protein 25 | C, I | protein | 75 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptosomal-associated protein 25 | D, J | protein | 64 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptotagmin-1 | E, F, K | protein | 279 | Rattus norvegicus | P21707 (AlphaFold model) |
Sequence of entity 1 (A, G), FASTA
>5KJ7_1 Vesicle-associated membrane protein 3 (chains A, G)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW
Sequence of entity 2 (B, H), FASTA
>5KJ7_2 Syntaxin-1A (chains B, H)
ALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSD
TKKAVK
Sequence of entity 3 (C, I), FASTA
>5KJ7_3 Synaptosomal-associated protein 25 (chains C, I)
NELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHIN
QDMKEAEKNLKDLGK
Sequence of entity 4 (D, J), FASTA
>5KJ7_4 Synaptosomal-associated protein 25 (chains D, J)
ARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRAT
KMLG
Sequence of entity 5 (E, F, K), FASTA
>5KJ7_5 Synaptotagmin-1 (chains E, F, K)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNG
KRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGY
NSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 19 |
Primary citation
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Lyubimov, A.Y., Uervirojnangkoorn, M., Zeldin, O.B. et al. Elife (2016) 5. DOI 10.7554/eLife.18740 · PubMed
Other PDB entries of the same protein (UniProt P63025 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5KJ8 4.1 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from…
Browse structure collections
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