Structural biology

Conservation in vesicle coats

Coat proteins of vesicles involved in intracellular membrane trafficking have closely related molecular architectures. The structure of COPI extends known similarities, and strengthens the case for a common evolutionary origin.

Vesicles that transport cargo between intracellular compartments bud from the membrane of one compartment and fuse with the membrane of its target compartment. Vesiculation requires the introduction of local curvature into a lipid bilayer, typically by assembly of a closed protein shell — the coat — linked specifically to membrane-anchored proteins. Previous work has revealed some noteworthy similarities among coat proteins from different routes for membrane traffic. Reporting in Cell, Lee and Goldberg1 now describe the structures of components of coat-protein I (COPI)-coated vesicles. Their results clarify the characteristics required of a protein assembly that vesiculates membranes.

Three routes for membrane traffic, conserved in their molecular components from yeast to human, are of particular physiological interest. Clathrin-coated vesicles transport cargo from the cell membrane to endosomes, and between endosomes and the trans-Golgi network2. COPII-coated vesicles export newly synthesized proteins from the endoplasmic reticulum3. COPI-coated vesicles carry retrograde cargo between compartments of the Golgi apparatus4. The structures and assembly properties of clathrin5 and COPII6 components have revealed some noteworthy similarities between the two and suggested common evolutionary origins. Lee and Goldberg's data extend the pattern of similarities to COPI.

Clathrin is a trimer, with three molecular 'legs' radiating from a compact hub in a configuration known as a triskelion (Fig. 1a). The tip of each leg consists of the amino-terminal domain of the clathrin polypeptide chain, together with a β-propeller fold consisting of 'WD40' repeats. The legs themselves are α-helical zigzags, known as α-solenoids because of the (irregular) superhelical packing of their α-helices. Repeats of this kind generate stiff but still-compliant structures, which allow the formation of large-scale bends from small, energetically negligible, local perturbations in successive helix–helix contacts.

Figure 1: Schematic representation of coat proteins and their assemblies.
figure1

The basic structural elements of the assembly units of clathrin, COPII and COPI are α-solenoids (thick, curving lines) and β-propellers (cylinders). a, Two views of a clathrin triskelion. The N-terminal, β-propeller domains are at the tips of the legs. b, Packing of triskelions in an icosahedral clathrin coat, one of many lattices formed by clathrin5. There is a triskelion at each vertex, but only two are shown. c, The dimeric Sec31/Sec13 complex forms the coat of COPII vesicles6. The N-terminal, β-propeller domain of Sec31 is at the tip of the rod-like complex. A C-terminal segment of Sec31 is not present in the structure shown. d, Packing of Sec31/Sec13 in a COPII cuboctahedral lattice. The Sec31 β-propellers pack around the four-coordinated vertices6,7. e, Lee and Goldberg1 report the crystal structure of the COPI assembly unit, a complex of the N-terminal half of the β′-chain and a central segment of the α-chain. f, The authors propose this model for the lattice of a COPI coat. Although the COPI triskelion is present in their crystal structure, the lattice symmetry and packing of triskelions within the lattice are speculative. The lattices are shown roughly to scale; the outer diameter of the clathrin coat in b is about 90 nm.

Clathrin triskelions assemble into open lattices, in which each leg extends around three lattice edges (Fig. 1b). Gentle bending of the legs allows the generation, from uniform components that make essentially identical local contacts, of lattices with a triskelion hub at each vertex but with a considerable range of diameters. The amino-terminal domains project inwards to contact membrane-associated adaptor proteins, which in turn recruit the cargo proteins.

COPII is a set of four proteins organized as two heterodimers: the Sec31/Sec13 pair generates the lattice of a coat; and the Sec23/Sec24 dimer is the cargo adaptor. Sec13 is a WD40 β-propeller. Sec31 also has an amino-terminal β-propeller, followed by an α-solenoid, rather like clathrin. Unlike clathrin, however, the β-propellers of these proteins form the vertices. Previous work6,7 has shown how the assembly unit of COPII, composed mainly of Sec31 plus Sec13, can generate a set of symmetrical lattices in which four edges converge on a two-fold symmetrical vertex (Fig. 1c,d). Variability in the curvature of the α-solenoid elements can allow for variable diameters of the COPII coat, to accommodate cargoes of various sizes. The carboxy-terminal half of Sec31, which recruits Sec23/Sec24, projects flexibly inward, towards the membrane.

COPI is a complex of seven proteins: α-, β-, β′-, γ-, δ-, ɛ- and ζ-COP. Of these, three — α-, β′- and ɛ-COP — make up a stable, shell-forming heterotrimer, and the remaining four form a complex similar to heterotetrameric clathrin adaptors. Lee and Goldberg1 have determined crystal structures of an αβ′-subcomplex; it consists of most of the β′-chain (two tandem WD40 β-propellers followed by an α-solenoid) and a central fragment of the α-chain (a further α-solenoidal segment). This basic unit makes a triskelion-like trimer, with the dual β-propellers of β′-COP at its centre and the overlapping, antiparallel α-solenoids of the α- and β′-chains radiating outwards (Fig. 1e). The amino-terminal part of α-COP, which is missing from the structure, includes a further predicted β-propeller; a continuation of the legs, therefore, will place such a domain at their tips, just as in clathrin.

The authors (and another team8) also report the structure of the carboxy-terminal part of α-COP in complex with ɛ-COP: the two polypeptide chains form an intertwined, α-solenoid handshake. This subcomplex is linked to the αβ′-subcomplex by a flexible α-chain segment, and a plausible suggestion is that it projects inwards from the αβ′-lattice to recruit the βγδζ-adaptor complex. COPI vesicles seen by electron microscopy of thin-sectioned cells seem to be relatively uniform in diameter9, so the range of lattice diameters to which the COPI αβ′-triskelions must adapt may be relatively small. Lee and Goldberg propose a model for such a lattice, with an αβ′- triskelion at each vertex and with postulated two-fold contacts between such triskelions at the middle of each edge (Fig. 1f). Whether this model is correct can be verified by analysis of isolated or reconstituted COPI coats by electron cryomicroscopy or tomography.

Lee and Goldberg's results show that clathrin, COPI and COPII have certain architectural principles in common; these include the structural motifs that contribute to the shell and the characteristics of the linkage between the coat and the membrane. The conservation of α-solenoid and β-propeller substructures between these three coat proteins is probably also a sign of their common evolutionary origin. The combination seems unlikely to be coincidental, even though the roles of the β-propeller components vary among the different coat proteins. A reason for the evolutionary persistence of the α-solenoid could be its suitability for creating lattices of variable diameter. A clearer view of potential missing links may be necessary to establish a common origin with confidence.

The same α-solenoid and β-propeller substructures (including Sec13 itself) make up a large part of another membrane-curving assembly (the scaffold of the nuclear pore10), which may also have been derived from the common vesicle-coat precursor. The nuclear pore has a fixed geometry, however, and the α-solenoids of nuclear porin proteins curve back on themselves to form a more rigid structure than the completely extended legs of a clathrin triskelion.

The flexible tethers that link the COP coats and clathrin to adaptor components make minimal demands on the organization of the vesicle and thus allow for a wide selection of protein and lipid cargo. The relatively open lattices of all three types of coat allow access to the underlying membrane and accommodate variable projections from its cytoplasmic surface. The clathrin lattice is so open that it does not constrict the 'neck' of the budding vesicle tightly enough to drive fission; it recruits a large protein called dynamin, which has GTPase-enzyme activity, to finish the job11.

There is one further, noteworthy, common principle of vesicle-coat biochemistry. A reversible assembly–disassembly cycle that allows reuse of the coat components requires the input of free energy. COPI, COPII and clathrin coats meet this requirement by harnessing hydrolysis of the nucleotides GTP and ATP. Assembly and release of COPI and COPII are linked to the GTP-hydrolysis cycle of a small GTPase enzyme — Arf1 in the case of COPI12 and Sar1 in the case of COPII13. COPI is itself a crucial component of the Arf-GTPase activating complex14. Clathrin recruits the Hsc70 ATPase, which dissociates the coat after dynamin has pinched off the internal vesicle15. The unified picture of carrier-vesicle properties that derives both from these parallels and from the recent structural studies of COPI components1 enhances the likelihood that analysis of one transport system will inform characterization of the others.

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Harrison, S., Kirchhausen, T. Conservation in vesicle coats. Nature 466, 1048–1049 (2010). https://doi.org/10.1038/4661048a

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