5CCI: Mg2+-bound synaptotagmin-1 SNARE complex
Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form). Determined by X-ray diffraction at 4.1 Å resolution. Released 12 Aug 2015.
- Method
- X-ray diffraction
- Resolution
- 4.1 Å
- Organism
- Rattus norvegicus
- Chains
- 6
- Atoms
- 6,406
- Mol. weight
- 96.16 kDa
- Ligands
- MG
- Released
- 12 Aug 2015
Explore 5CCI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5CCI contains 20 α-helices and 38 β-strands across 6 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: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-88 | 60 | |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 192-255 | 64 | |
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 | 141-201 | 61 | |
Chain E: 8 helices, 20 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 | 264-268 | 5 | |
| β-strand | 275-283 | 9 | 3 |
| β-strand | 288-297 | 10 | 3 |
| α-helix | 299-301 | 3 | |
| β-strand | 308 | 1 | 4 |
| β-strand | 310-318 | 9 | 5 |
| β-strand | 321-327 | 7 | 5 |
| β-strand | 334 | 1 | 4 |
| β-strand | 338-346 | 9 | 3 |
| α-helix | 352-354 | 3 | |
| β-strand | 356-363 | 8 | 5 |
| β-strand | 372-379 | 8 | 5 |
| α-helix | 385-395 | 11 | |
| β-strand | 401-406 | 6 | 3 |
| β-strand | 408 | 1 | 5 |
| α-helix | 410-417 | 8 | |
Chain F: 8 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 144-152 | 9 | 6 |
| β-strand | 157-166 | 10 | 6 |
| α-helix | 168-170 | 3 | |
| β-strand | 179-185 | 7 | 7 |
| α-helix | 190-192 | 3 | |
| β-strand | 193-194 | 2 | 7 |
| α-helix | 195-199 | 5 | |
| β-strand | 205-212 | 8 | 6 |
| α-helix | 216-219 | 4 | |
| β-strand | 223-230 | 8 | 7 |
| β-strand | 239-241 | 3 | 7 |
| β-strand | 244-246 | 3 | 7 |
| β-strand | 256-261 | 6 | 6 |
| β-strand | 275-283 | 9 | 8 |
| β-strand | 288-297 | 10 | 8 |
| α-helix | 299-301 | 3 | |
| β-strand | 310-318 | 9 | 9 |
| β-strand | 321-327 | 7 | 9 |
| β-strand | 338-346 | 9 | 8 |
| α-helix | 352-354 | 3 | |
| β-strand | 356-363 | 8 | 9 |
| β-strand | 374-379 | 6 | 9 |
| α-helix | 385-395 | 11 | |
| β-strand | 401-406 | 6 | 8 |
| β-strand | 408 | 1 | 9 |
| α-helix | 410-417 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vesicle-associated membrane protein 2 | A | protein | 63 | Rattus norvegicus | P63045 (AlphaFold model) |
| Syntaxin-1A | B | protein | 67 | Rattus norvegicus | P32851 (AlphaFold model) |
| Synaptosomal-associated protein 25 | C | protein | 77 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptosomal-associated protein 25 | D | protein | 65 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptotagmin-1 | E, F | protein | 281 | Rattus norvegicus | P21707 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>5CCI_1 Vesicle-associated membrane protein 2 (chains A)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR
KYW
Sequence of entity 2 (B), FASTA
>5CCI_2 Syntaxin-1A (chains B)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK
Sequence of entity 3 (C), FASTA
>5CCI_3 Synaptosomal-associated protein 25 (chains C)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK
Sequence of entity 4 (D), FASTA
>5CCI_4 Synaptosomal-associated protein 25 (chains D)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG
Sequence of entity 5 (E, F), FASTA
>5CCI_5 Synaptotagmin-1 (chains E, F)
KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRK
TLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWR
DLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNG
KRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGY
NSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
Primary citation
Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Zhou, Q., Lai, Y., Bacaj, T. et al. Nature (2015) 525:62-67. DOI 10.1038/nature14975 · PubMed
Other PDB entries of the same protein (UniProt P63045 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1N7S 1.45 Å, High Resolution Structure of a Truncated Neuronal SNARE Complex
- 5W5C 1.85 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex
- 6WVW 2.11 Å, Crystal structure of the R59P-SNAP25 containing SNARE complex
- 1KIL 2.3 Å, Three-dimensional structure of the complexin/SNARE complex
- 1SFC 2.4 Å, Neuronal synaptic fusion complex
- 5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
- 6A30 2.79 Å, Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region
- 3HD7 3.4 Å, Helical extension of the neuronal snare complex into the membrane, spacegroup C 1 2 1
- 5CCG 3.5 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form)
- 7UDB 3.5 Å, Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2
- 5CCH 3.6 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
- 6IP1 3.9 Å, alpha-SNAP-SNARE subcomplex in the whole 20S complex
Browse structure collections
About this viewer
MolViewer shows 5CCI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.