Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker - PubMed (original) (raw)

Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker

E ter Haar et al. Cell. 1998.

Abstract

Clathrin triskelions form the lattice that organizes recruitment of proteins to coated pits and helps drive vesiculation of the lipid bilayer. We report the crystal structure at 2.6 A resolution of a 55 kDa N-terminal fragment from the 190 kDa clathrin heavy chain. The structure comprises the globular "terminal domain" and the linker that joins it to the end of a triskelion leg. The terminal domain is a seven-blade beta propeller, a structure well adapted to interaction with multiple partners, such as the AP-1 and AP-2 sorting adaptor complexes and the nonvisual arrestins. The linker is an alpha-helical zigzag emanating from the propeller domain. We propose that this simple motif may extend into the rest of the clathrin leg.

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Figures

Figure 1

Figure 1. Schematic Representations of a Clathrin Triskelion, Showing Structural Subdivisions of a Leg and the Packing of a Triskelion in the Lattice of a Coat

(A) Correspondence between molecular morphology and positions in the polypeptide chain. The diagram is based on results from single-molecule electron microscopy, limited proteolysis, sizing chromatography, and primary structure determination (Schmid et al., 1982; Kirchhausen et al., 1983; Ungewickell, 1983; Kirchhausen and Harrison, 1984; Kirchhausen et al., 1987a). Selective proteolytic cleavage sites in the native molecule are boxed. (B) A typical lattice for a clathrin coat, with a single triskelion superimposed. Each leg of a triskelion contributes to two adjacent edges. The linker and terminal domain project inwards. The figure is based on results from electron microscopy (Crowther and Pearse, 1981; Heuser and Kirchhausen, 1985; Vigers et al., 1986).

Figure 2

Figure 2. Overall Structure of the Terminal Domain and Part of the Linker from the Rat Clathrin Heavy Chain The ribbon diagram shows the structure of the 55 kDa fragment of clathrin

The terminal domain (yellow) is a β propeller. The linker (red) is an α zigzag. The views in (A) and (B) include the first 487 amino acid residues of the clathrin heavy chain, which are visible in the electron density map in all the monomers in the crystallographic asymmetric unit. The view in (B) represents a 90° counterclockwise rotation about the vertical axis of the view in (A). The α helices are numbered α1 to α10. Blade 5 of the β propeller is labeled for orientation; loops 5a, 5b, 5c, and 5d project from the “bottom” surface of this blade. Figure was made with RIBBONS (Carson, 1991).

Figure 3

Figure 3. Ribbon Diagram of the Clathrin β Propeller Terminal Domain

The β propeller spans amino acid residues M1–E330. It has seven blades (1–7) organized sequentially in a counterclockwise direction and viewed here looking from the “top” to the “bottom” surface along the pseudo-7-fold axis. Within each blade, the orientations of the four β strands (a, b, c, and d) alternate, starting with the innermost strand, “a,” which runs from top to bottom, and ending with the outermost strand, “d,” which runs from bottom to top. Closure is achieved in blade 7 by the contributions of β strand 7d (residues P6 to H12) derived from the N terminus of the polypeptide chain. Figure was made with RIBBONS (Carson, 1991).

Figure 4

Figure 4. Structure-Based Sequence Alignment of Rat Clathrin Heavy Chain

(A) The sequence of the heavy chain (residues M1–E494) is shown with the elements of secondary structure indicated above the alignment. Yellow arrows mark β strands in the propeller; red cylinders, α helices in the linker. (B) Alignment of the seven blades within the β propeller of the terminal domain. The approximate boundaries of the strands are highlighted. ϕ designates conserved hydrophobic residues; W and D designate Trp and Asp. For comparison, the position of the WD repeat in bovine rod β transducin is shown (Sondek et al., 1996).

Figure 5

Figure 5. Structural Alignment of the Seven Blades in the Clathrin β Propeller

The figure shows a superposition of Cα traces for the seven blades of the clathrin β propeller, aligned using strands βb and βc of each blade. Blades 2, 3, 6, and 7 (yellow) have the shortest loops between β strands. Blades 1, 4, and 5 (red, green, and blue) have at least one long loop projecting from the top or the bottom surface of the β propeller. (A) and (B) correspond to views rotated by about 50° with respect to each other. (C) shows blade 1 of the β propeller from β-transducin (Sondek et al., 1996).

Figure 6

Figure 6. Mapping of Interaction Sites in Clathrin Terminal Domain Required for the Association with Nonvisual Arrestins

Residues of clathrin that participate in contacts with the C-terminal arm of arrestin3 and β-arrestin (Goodman et al., 1997) are shown in red in the space-filling representations (A and B) and as ball and stick models in the ribbon diagram (C). In (A) and (B), residues M1 to K100 are highlighted in gray; these correspond to blades 1 and 2 and to strand 7a. This segment by itself can bind to arrestin3 and β-arrestin (Goodman et al., 1997). The rest of the domain (residues A101 to E330) is yellow. The views in (A) and (B) are similar, respectively, to the top view in Figure 3 and to the side view in Figure 2A. The amino acid sequence of the segment of arrestin3 that binds this site is TNLIEFETN (Krupnick et al., 1997). Figure was made with RIBBONS (Carson, 1991).

Figure 7

Figure 7. Structure of the α zigzag Region in the Clathrin Linker

(A) Superposition of Cα traces from the helical region of the three monomers (red, blue, green) in the crystallographic asymmetric unit. The superposition was obtained by alignment of the β propeller domains (not shown). (B) Cylinder representation of the α zigzag region of a monomer to show the overall right-handed twist in the linker region. Figure was made with Setor (Evans, 1993).

Figure 8

Figure 8. Relationship between the Clathrin Triskelion and the Structure of the Terminal Domain and Linker

Clathrin was deposited onto freshly cleaved mica by spraying in 50% glycerol, rotary shadowed with Pt, and visualized by electron microscopy (see Heuser and Kirchhausen, 1985). The ribbon diagram corresponds to the terminal domain and linker.

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References

    1. Boll W, Ohno H, Songyang Z, Rapoport I, Cantley LC, Bonifacino JS, Kirchhausen T. Sequence requirements for the recognition of tyrosine-based endocytic signals by clathrin AP-2 complexes. EMBO J. 1996;15:5789–5795. - PMC - PubMed
    1. Brünger AT. X-PLOR Version 3.1: A System for X-Ray Crystallography and NMR. New Haven, Connecticut: Yale University Press; 1992.
    1. Carson M. Ribbons 2.0. J Appl Crystallogr. 1991;24:958–961.
    1. Clairmont KB, Boll W, Ericsson M, Kirchhausen T. A role for the hinge/ear domain of the beta chains in the incorporation of AP complexes into clathrin-coated pits and coated vesicles. Cell Mol Life Sci. 1997;53:611–619. - PMC - PubMed
    1. Collaborative Computational Project Number 4. The CCP4 Suite: Programs for Protein Crystallography. Acta Crystallogr D. 1994;50:760–763. - PubMed

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