2N1T: Vesicle-associated membrane protein 2

Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution. Determined by solution NMR. Released 3 Jun 2015.

Method: Solution NMR
Organisms: Rattus norvegicus, Homo sapiens
Chains: 5
Atoms: 3,591
Mol. weight: 51.43 kDa
Released: 3 Jun 2015

Explore 2N1T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2N1T contains 11 α-helices and 10 β-strands across 5 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	30-91	62

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	191-256	66

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-81	70

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	141-200	60

Chain E: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	267-269	3
β-strand	275-282	8	1
β-strand	288-297	10	1
α-helix	299-301	3
β-strand	311-318	8	2
β-strand	321-327	7	2
α-helix	328-330	3
β-strand	338-346	9	1
α-helix	349-352	4
β-strand	355-362	8	2
α-helix	370-371	2
β-strand	372-379	8	2
α-helix	384-395	12
β-strand	397	1	1
β-strand	403-406	4	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	69	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	B	protein	72	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	C	protein	77	Homo sapiens	P60880 (AlphaFold model)
Synaptosomal-associated protein 25	D	protein	74	Homo sapiens	P60880 (AlphaFold model)
Synaptotagmin-1	E	protein	156	Homo sapiens	P21579 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2N1T_1 Vesicle-associated membrane protein 2 (chains A)
NLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL
KRKYWWKNL

Sequence of entity 2 (B), FASTA

>2N1T_2 Syntaxin-1A (chains B)
SKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERA
VSDTKKAVKYQS

Sequence of entity 3 (C), FASTA

>2N1T_3 Synaptosomal-associated protein 25 (chains C)
MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNH
INQDMKEAEKNLKDLGK

Sequence of entity 4 (D), FASTA

>2N1T_4 Synaptosomal-associated protein 25 (chains D)
GGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKT
RIDEANQRATKMLG

Sequence of entity 5 (E), FASTA

>2N1T_5 Synaptotagmin-1 (chains E)
SGGGGGILEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKR
LKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNS
TGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLA

Primary citation

Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Brewer, K.D., Bacaj, T., Cavalli, A. et al. Nat Struct Mol Biol (2015) 22:555-564. DOI 10.1038/nsmb.3035 · 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

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