3HD7: Vesicle-associated membrane protein 2
Helical extension of the neuronal snare complex into the membrane, spacegroup C 1 2 1. Determined by X-ray diffraction at 3.4 Å resolution. Released 14 Jul 2009.
- Method
- X-ray diffraction
- Resolution
- 3.4 Å
- Organism
- Rattus norvegicus
- Chains
- 8
- Atoms
- 5,322
- Mol. weight
- 81.12 kDa
- Ligands
- GGG
- Released
- 14 Jul 2009
Explore 3HD7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3HD7 contains 8 α-helices and 0 β-strands across 8 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 E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-112 | 83 | |
Chains B and F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 190-283 | 94 | |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-79 | 71 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 140-195 | 56 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-79 | 68 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 140-198 | 59 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vesicle-associated membrane protein 2 | A, E | protein | 91 | Rattus norvegicus | P63045 (AlphaFold model) |
| Syntaxin-1A | B, F | protein | 109 | Rattus norvegicus | P32851 (AlphaFold model) |
| Synaptosomal-associated protein 25 | C, G | protein | 80 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptosomal-associated protein 25 | D, H | protein | 68 | Rattus norvegicus | P60881 (AlphaFold model) |
Sequence of entity 1 (A, E), FASTA
>3HD7_1 Vesicle-associated membrane protein 2 (chains A, E)
GSHMRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLK
RKYWWKNLKMMIILGVICAIILIIIIVYFST
Sequence of entity 2 (B, F), FASTA
>3HD7_2 Syntaxin-1A (chains B, F)
GSHMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEH
AVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIIIASTIGGIFG
Sequence of entity 3 (C, G), FASTA
>3HD7_3 Synaptosomal-associated protein 25 (chains C, G)
GSHMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEG
MNHINQDMKEAEKNLKDLGK
Sequence of entity 4 (D, H), FASTA
>3HD7_4 Synaptosomal-associated protein 25 (chains D, H)
GSHMARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEAN
QRATKMLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GGG | glycylglycylglycine | C6 H11 N3 O4 | 3 |
Water and common crystallization additives (SO4) are not listed.
Primary citation
Helical extension of the neuronal SNARE complex into the membrane. Stein, A., Weber, G., Wahl, M.C. et al. Nature (2009) 460:525-528. DOI 10.1038/nature08156 · 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
- 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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