3IPD: Vesicle-associated membrane protein 2

Helical extension of the neuronal SNARE complex into the membrane, spacegroup I 21 21 21. Determined by X-ray diffraction at 4.8 Å resolution. Released 1 Sept 2009.

Method: X-ray diffraction
Resolution: 4.8 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 5,242
Mol. weight: 79.79 kDa
Released: 1 Sept 2009

Explore 3IPD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IPD contains 18 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	31-68	38
α-helix	72-97	26
α-helix	102-111	10

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	195-217	23
α-helix	219-276	58

Chains C and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-77	57

Chains D and H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	143-146	4
α-helix	149-186	38
α-helix	189-196	8

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	195-217	23
α-helix	219-278	60

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

>3IPD_1 Vesicle-associated membrane protein 2 (chains A, E)
GSHMRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLK
RKYWWKNLKMMIILGVICAIILIIIIVYFST

Sequence of entity 2 (B, F), FASTA

>3IPD_2 Syntaxin-1A (chains B, F)
GSHMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEH
AVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIIIASTIGGIFG

Sequence of entity 3 (C, G), FASTA

>3IPD_3 Synaptosomal-associated protein 25 (chains C, G)
GSHMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEG
MNHINQDMKEAEKNLKDLGK

Sequence of entity 4 (D, H), FASTA

>3IPD_4 Synaptosomal-associated protein 25 (chains D, H)
GSHMARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEAN
QRATKMLG

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
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

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