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spinqualitylabelsall models PDB ID 2nps Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2nps, resolution 2.50Å ()
Gene:	Vamp4_predicted (Mus musculus), syntaxin 13 (Rattus norvegicus), Vti1a (Rattus norvegicus), STX6 (Homo sapiens)
Structural annotation: Resources: InterPro : Ipr001388, Ipr010989, Ipr006012, Ipr000727, Ipr006011, Ipr007705, Ipr015260 Pfam : PF00957, PF05739, PF05008 UniProt : O70480, O70319, Q9JI51, O43752
Functional annotation: Cellular component: integral to membrane membrane cytoplasmic vesicle synapse cell junction Golgi apparatus clathrin-coated vesicle trans-Golgi network early endosome integral to plasma membrane perinuclear region of cytoplasm plasma membrane Biological process: vesicle-mediated transport intracellular protein transport protein transport transport endosome organization and biogenesis Golgi vesicle transport vesicle fusion Molecular function: protein binding protein transporter activity
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

Introduction

Important biological processes, such as synaptic transmission and cellular trafficking in Eukaryotes require SNARE proteins that are thought to play a crucial role in membrane fusion.^[1][2][3][4] To connect membranes and allow their fusion, SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) proteins assemble into a core-complex of four parallel helices.^[5][6][7] The SNARE complex assembly is mediated by a conserved SNARE motif consisting of 60-70 amino acids. ^[8] SNAREs can be divided into two categories: the v-(vesicle) SNAREs, which are found in the vesicle membrane and the t-(target) SNAREs, which are anchored in the target membrane.^[9]

The best-studied SNAREs are the neuronal and the early endosomal SNARE complexes. The Neuronal SNARE complex mediates exocytosis of synaptic vesicles in the neurons and includes the vesicle protein synaptobrevin (also called VAMP), the membrane proteins SNAP-25 and syntaxin 1.^[7] The early endosomal SNARE complex includes syntaxin 6, syntaxin 13, vti1a and VAMP4 and is responsible for homotypic fusion of early endosomes.^[10] It has been shown that the crystal structure of the early endosomal SNARE complex resembles that of the neuronal and late endosomal complexes, but differs in surface side-chain interactions.

Membrane fusion mechanism

Membrane fusion mechanism

Membrane Fusion requires the assembly of the core complex. Free t-SNAREs that are organized in clusters first assemble into acceptor complexes thanks to SM (Sec1/Munc18-related) proteins. Acceptor complexes can then interact with the v-SNAREs through the N-terminal domain of the SNARE motif. This enables the formation of four-helical trans-complexes, in which only the N-terminal portions of the SNARE motifs are bound. This binding evolves from a loose to a tight state, thus leading to the formation of a fusion pore. During the fusion, the conformation relaxes to a cis-configuration. Cis-complexes dissociate thanks to proteins and cofactors (SNAPs). T- and v-SNAREs can be separated and recycled.^[11]

Structure

SNARE domain

The SNARE domain is approximately 60-70 residues long and is located immediately adjacent to a C-terminal transmembrane anchor. It contains a repeating heptad pattern of hydrophobic residues. Their orientation places them in an alpha-helical structure so that all the hydrophobic side chains are located on the same face of the helix.^[5][12][7] SNARE domains allow the four SNAREs protein to assemble into parallel four-helix bundles. This parallel arrangement brings the transmembrane anchors and the membranes closer. ^[13]

“0”-layer

Topology of the 16 layers of the SNARE complex

The centre of the four-helix bundle is constituted of 16 layers. These layers are composed of , which are perpendicular to the axis of the four-helix bundle, except for the central “0”-layer. This last one consists of three glutamine (Q) and one arginine (R) highly conserved residues. Those highly conserved residues have led to a new classification of SNAREs into Q- and R-SNAREs. ^[14] Almost all membrane fusion reactions require one R-SNARE and three Q-SNAREs: Qa, Qb and Qc.^[15][16] In many cases, the R-SNARE is in the vesicle, and the three Q-SNAREs are in the target membrane. For the early endosomal SNARE complex, syntaxin 13, vti1a, syntaxin 6, and VAMP4 were respectively classified as Qa-, Qb-, Qc- and R-SNAREs.

Structure of the early endosomal SNARE complex 2NPS

Crystal structure of the early endosomal SNARE complex. (A) Backbone overlay of the early endosomal SNARE complex (in color) and the neuronal SNARE complex (gray). (B) N- to C-terminal view of the 0 layer containing the unusual aspartate in vti1a. (Color, early endosomal SNARE complex; gray, neuronal SNARE complex.) (C) Residue E143 builds a salt bridge with the residue S179. The residue E143 is also sandwiched by residues V182 and V140, which strengthen polar interactions. In the late endosomal and in the neuronal SNARE complex, this glutamate is conserved and interacts with a conserved arginine that occupies the position equivalent to V182. (D) View of the 0 layer, including hydrogen bonds with surface residues and water molecules.

The early endosomal SNARE complex forms a four-helix bundle with a left-handed superhelical twist. The position of the Qa-, Qb-, Qc-, and R-SNAREs is the same in the neuronal and late endosomal complexes.^[7][5] As mentioned above, an unconventional layer of hydrophilic residues – the “0”-layer – constituted of three glutamines and one arginine, characterizes the center of all SNARE complexes. However, in vti1a an aspartate residue substitutes the glutamine. The aspartate occupies the same position as the glutamine in the neuronal and late endosomal complexes, and is involved in a similar organization of hydrogen bonds with the other layer of amino acids. Moreover, in vti1a, of the ‘0' layer also interacts with at the surface of the vti1a helix and with a water molecule. Also,