6IP1: Vesicle-associated membrane protein 2

Name: PDB 6IP1: alpha-SNAP-SNARE subcomplex in the whole 20S complex
Published: 2019-04-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

alpha-SNAP-SNARE subcomplex in the whole 20S complex. Determined by electron microscopy at 3.9 Å resolution. Released 24 Apr 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Rattus norvegicus, Bos taurus
Chains: 8
Atoms: 11,245
Mol. weight: 199.94 kDa
Released: 24 Apr 2019

Explore 6IP1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IP1 contains 76 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.

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-82	54

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	193-227	35
α-helix	231-251	21

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	18-36	19
α-helix	38-66	29
α-helix	69-76	8
α-helix	77-79	3

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-200	58

Chains E, F and H: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	6-19	14
α-helix	24-26	3
α-helix	40-54	15
α-helix	58-74	17
α-helix	78-89	12
α-helix	92-94	3
α-helix	97-112	16
α-helix	118-133	16
α-helix	138-154	17
α-helix	158-174	17
α-helix	178-193	16
α-helix	202-211	10
α-helix	222-231	10
α-helix	234-237	4
α-helix	240-251	12
α-helix	258-267	10
α-helix	274-294	21

Chain G: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	6-19	14
α-helix	24-26	3
α-helix	40-54	15
α-helix	58-74	17
α-helix	82-89	8
α-helix	92-94	3
α-helix	97-112	16
α-helix	118-133	16
α-helix	138-154	17
α-helix	158-174	17
α-helix	178-193	16
α-helix	203-211	9
α-helix	222-231	10
α-helix	234-237	4
α-helix	240-251	12
α-helix	258-267	10
α-helix	274-294	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vesicle-associated membrane protein 2	A	protein	97	Rattus norvegicus	P63045 (AlphaFold model)
Syntaxin-1A	B	protein	254	Rattus norvegicus	P32851 (AlphaFold model)
Synaptosomal-associated protein 25	C	protein	102	Rattus norvegicus	P60881 (AlphaFold model)
Synaptosomal-associated protein 25	D	protein	83	Rattus norvegicus	P60881 (AlphaFold model)
Alpha-soluble NSF attachment protein	E, F, G, H	protein	309	Bos taurus	P81125 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6IP1_1 Vesicle-associated membrane protein 2 (chains A)
GSHMSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERD
QKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLK

Sequence of entity 2 (B), FASTA

>6IP1_2 Syntaxin-1A (chains B)
GSKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHS
AILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQ
HSTLSRKFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFAS
GIIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEH
AVDYVERAVSDTKK

Sequence of entity 3 (C), FASTA

>6IP1_3 Synaptosomal-associated protein 25 (chains C)
GSMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLE
RIEEGMDQINKDMKEAEKNLTDLGKFCGLCVCPCNKLKSSDA

Sequence of entity 4 (D), FASTA

>6IP1_4 Synaptosomal-associated protein 25 (chains D)
GSQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIME
KADSNKTRIDEANQRATKMLGSG

Sequence of entity 5 (E, F, G, H), FASTA

>6IP1_5 Alpha-soluble NSF attachment protein (chains E, F, G, H)
GSMRGSHHHHHHGSMDNSGKEAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYA
RAANMFKMAKNWSAAGSAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMR
AIEIYTDMGRFTIAAKHHISIAEIYETELVDIEKAIAHYEQSADYYKGEESNSSANKCLL
KVAGYAAQLEQYQKAIDIYEQVGTNAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQ
KYEELFPAFSDSRECKLMKKLLEAHEEQNVDSYTEAVKEYDSISRLDQWLTTMLLRIKKT
IQGDEEDLR

Primary citation

Mechanistic insights into the SNARE complex disassembly. Huang, X., Sun, S., Wang, X. et al. Sci Adv (2019) 5:eaau8164-eaau8164. DOI 10.1126/sciadv.aau8164 · 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)
5CCI 4.1 Å, Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form)

Browse structure collections

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