5W5C: Vesicle-associated membrane protein 2
Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex. Determined by X-ray diffraction at 1.85 Å resolution. Released 23 Aug 2017.
- Method
- X-ray diffraction
- Resolution
- 1.85 Å
- Organism
- Rattus norvegicus
- Chains
- 6
- Atoms
- 4,044
- Mol. weight
- 71.52 kDa
- Ligands
- MG
- Released
- 23 Aug 2017
Explore 5W5C in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5W5C contains 15 α-helices and 20 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 | 30-64 | 35 | |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 192-242 | 51 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 14-71 | 58 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 142-194 | 53 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 52-70 | 19 | |
| α-helix | 72-74 | 3 | |
Chain F: 8 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 144-152 | 9 | 1 |
| β-strand | 157-166 | 10 | 1 |
| β-strand | 179-180 | 2 | 2 |
| β-strand | 182 | 1 | 3 |
| β-strand | 183-184 | 2 | 4 |
| β-strand | 194 | 1 | 3 |
| β-strand | 205-212 | 8 | 1 |
| α-helix | 216-218 | 3 | |
| β-strand | 223-228 | 6 | 4 |
| β-strand | 229-230 | 2 | 2 |
| β-strand | 241-246 | 6 | 4 |
| β-strand | 256-260 | 5 | 1 |
| α-helix | 266-270 | 5 | |
| β-strand | 275-283 | 9 | 5 |
| β-strand | 288-297 | 10 | 5 |
| α-helix | 299-301 | 3 | |
| β-strand | 310-318 | 9 | 6 |
| β-strand | 321-327 | 7 | 6 |
| α-helix | 328-330 | 3 | |
| β-strand | 338-346 | 9 | 5 |
| α-helix | 349-352 | 4 | |
| β-strand | 355-363 | 9 | 6 |
| α-helix | 364-366 | 3 | |
| β-strand | 372-379 | 8 | 6 |
| α-helix | 384-395 | 12 | |
| β-strand | 401-406 | 6 | 5 |
| β-strand | 408 | 1 | 6 |
| α-helix | 410-417 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vesicle-associated membrane protein 2 | A | protein | 40 | 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) |
| Complexin-1 | E | protein | 83 | Rattus norvegicus | P63041 (AlphaFold model) |
| Synaptotagmin-1 | F | protein | 282 | Rattus norvegicus | P21707 |
Sequence of entity 1 (A), FASTA
>5W5C_1 Vesicle-associated membrane protein 2 (chains A)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDR
Sequence of entity 2 (B), FASTA
>5W5C_2 Syntaxin-1A (chains B)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK
Sequence of entity 3 (C), FASTA
>5W5C_3 Synaptosomal-associated protein 25 (chains C)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK
Sequence of entity 4 (D), FASTA
>5W5C_4 Synaptosomal-associated protein 25 (chains D)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG
Sequence of entity 5 (E), FASTA
>5W5C_5 Complexin-1 (chains E)
MEFVMKQALGGATKDMGKMLGGDEEKDPDAAKKEEERQEALRQAEEERKAKYAKMEAERE
VMRQGIRDKYGIKKKEEREAEAQ
Sequence of entity 6 (F), FASTA
>5W5C_6 Synaptotagmin-1 (chains F)
EKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHR
KTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEW
RDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQN
GKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVG
YNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis. Zhou, Q., Zhou, P., Wang, A.L. et al. Nature (2017) 548:420-425. DOI 10.1038/nature23484 · 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
- 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
- 5CCI 4.1 Å, Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
Browse structure collections
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