Database accession: MF4411002
Name: Endosomal SNARE core complex (Vamp8 / Vti1-rp1 / Syntaxin-7 / Syntaxin-8)
PDB ID: 1gl2
Experimental method: X-ray (1.9 Å)
Assembly: heterotetramer
Source organism: Rattus norvegicus / Mus musculus
Primer publication of the structure:
Antonin W, Fasshauer D, Becker S, Jahn R, Schneider TR
Crystal structure of the endosomal SNARE complex reveals common structural principles of all SNAREs.
(2002) Nat. Struct. Biol. 9: 107-11
PMID: 11786915
Abstract:
SNARE proteins are crucial for intracellular membrane fusion in all eukaryotes. These proteins assemble into tight complexes that connect membranes and may induce fusion. The crystal structure of the neuronal core complex is represented by an unusually long bundle of four alpha-helices connected by 16 layers of mostly hydrophobic amino acids. Here we report the 1.9 A resolution crystal structure of an endosomal SNARE core complex containing four SNAREs: syntaxin 7, syntaxin 8, vti1b and endobrevin/VAMP-8. Despite limited sequence homology, the helix alignment and the layer structure of the endosomal complex are remarkably similar to those of the neuronal complex. However, subtle variations are evident that characterize different SNARE subfamilies. We conclude that the structure of the SNARE core complex is an evolutionarily conserved hallmark of all SNARE complexes and is intimately associated with the general role of SNAREs in membrane fusion.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
SNAP receptor activity Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
Biological process:
Cellular component:
lysosomal membrane The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
integral component of membrane The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
recycling endosome An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
Structural annotations of the participating protein chains.Entry contents: 4 distinct polypeptide molecules
Chains: A, B, C, D
Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.
Number of unique protein segments: 4
Name: Vesicle-associated membrane protein 8
Source organism: Rattus norvegicus
Length: 65 residues
Sequence:Sequence according to PDB SEQRESGSHMSAGNDRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQKVAR
UniProtKB AC: Q9WUF4 (positions: 2-66) Coverage: 65%
UniRef90 AC: UniRef90_O70404 (positions: 7-67)
Name: Syntaxin-7
Source organism: Mus musculus
Length: 65 residues
Sequence:Sequence according to PDB SEQRESGSHMHERESSIRQLEADIMDINEIFKDLGMMIHEQGDVIDSIEANVESAEVHVQQANQQLSRAAN
UniProtKB AC: O70439 (positions: 165-229) Coverage: 24.9%
UniRef90 AC: UniRef90_O15400 (positions: 168-229)
Name: Vesicle transport through interaction with t-SNAREs homolog 1B
Source organism: Mus musculus
Length: 65 residues
Sequence:Sequence according to PDB SEQRESGSHMNRATQSIERSHRIATETDQIGTEIIEELGEQRDQLERTKSRLVNTNENLSKSRKILRSMSR
UniProtKB AC: O88384 (positions: 136-200) Coverage: 28%
UniRef90 AC: UniRef90_O88384 (positions: 139-200)
Name: Syntaxin-8
Source organism: Rattus norvegicus
Length: 65 residues
Sequence:Sequence according to PDB SEQRESGSHMQEQDAGLDALSSIISRQKQMGQEIGNELDEQNEIIDDLANLVENTDEKLRTEARRVTLVDR
UniProtKB AC: Q9Z2Q7 (positions: 145-209) Coverage: 27.5%
UniRef90 AC: UniRef90_Q9Z2Q7 (positions: 152-209)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Complex evidence:
The structure shows the core domain of a SNARE complex (PMID: 11786915). SNARE complexes are formed by the parallel arrangement of four protein chains bound by coiled-coil interactions forming a four helix bundle (PMID: 9390521). Coiled coils are highly versatile folding units (PMID: 11166216), where the formation of the structure and the interaction between subunits is almost ubiquitously linked. This cooperative nature of binding and folding that results in a two-step process has been demonstrated for coiled coils with varying oligomeric state from dimers (PMID: 9811815) and trimers (PMID: 10933510) up to heptamers (PMID: 17030805). While the interaction and folding are linked, in certain cases there can be significant residual structure before association (PMID: 8401212). However, these residual structural elements usually encompass 1-2 turns of helices that serve as a 'nucleation site' driving interaction and helix formation (zipping up) (PMID: 17438295), thus even in these cases monomeric coiled coil subunits cannot be considered to have a stable structure.
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the Protein Data Bank.
