5W5D: Vesicle-associated membrane protein 2
Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 Aug 2017.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organism
- Rattus norvegicus
- Chains
- 6
- Atoms
- 3,217
- Mol. weight
- 56.03 kDa
- Ligands
- MG
- Released
- 23 Aug 2017
Explore 5W5D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5W5D contains 12 α-helices and 9 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 | 193-244 | 52 | |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-70 | 59 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 144-194 | 51 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-70 | 30 | |
| α-helix | 72-74 | 3 | |
Chain F: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 275-283 | 9 | 1 |
| β-strand | 288-297 | 10 | 1 |
| α-helix | 299-301 | 3 | |
| β-strand | 310-318 | 9 | 2 |
| β-strand | 321-327 | 7 | 2 |
| α-helix | 328-330 | 3 | |
| β-strand | 338-346 | 9 | 1 |
| α-helix | 352-354 | 3 | |
| β-strand | 355-363 | 9 | 2 |
| α-helix | 364-366 | 3 | |
| β-strand | 372-379 | 8 | 2 |
| α-helix | 385-395 | 11 | |
| β-strand | 401-406 | 6 | 1 |
| β-strand | 408 | 1 | 2 |
| 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 | 152 | Rattus norvegicus | P21707 |
Sequence of entity 1 (A), FASTA
>5W5D_1 Vesicle-associated membrane protein 2 (chains A)
GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDR
Sequence of entity 2 (B), FASTA
>5W5D_2 Syntaxin-1A (chains B)
MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVS
DTKKAVK
Sequence of entity 3 (C), FASTA
>5W5D_3 Synaptosomal-associated protein 25 (chains C)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK
Sequence of entity 4 (D), FASTA
>5W5D_4 Synaptosomal-associated protein 25 (chains D)
MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRA
TKMLG
Sequence of entity 5 (E), FASTA
>5W5D_5 Complexin-1 (chains E)
MEFVMKQALGGATKDMGKMLGGDEEKDPDAAKKEEERQEALRQAEEERKAKYAKMEAERE
VMRQGIRDKYGIKKKEEREAEAQ
Sequence of entity 6 (F), FASTA
>5W5D_6 Synaptotagmin-1 (chains F)
QEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTT
IKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRH
WSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
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
- 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
- 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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