PDBsum entry: 1b89

Clathrin

PDB id: 1b89

Contents

Protein chain

321 a.a. *

* Residue conservation analysis

PDB id:

1b89

Name:

Clathrin

Title:

Clathrin heavy chain proximal leg segment (bovine)

Structure:

Protein (clathrin heavy chain). Chain: a. Fragment: proximal leg. Engineered: yes. Other_details: the n-terminal poly-his tag (mhhhhhh) was not seen in the electron density

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.60Å R-factor: 0.254 R-free: 0.279

Authors:

J.A.Ybe,F.M.Brodsky,K.Hofmann,K.Lin,S.-H.Liu,L.Chen, T.N.Earnest,R.J.Fletterick,P.K.Hwang

Key ref:

J.A.Ybe et al. (1999). Clathrin self-assembly is mediated by a tandemly repeated superhelix. Nature, 399, 371-375. PubMed id: 10360576 DOI: 10.1038/20708

Date:

27-May-99 Release date: 04-Jun-99

Protein chain

P49951  (CLH1_BOVIN) -  Clathrin heavy chain 1

Seq: 1675 a.a.

Struc: 321 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane coat (1 term)
• Biological process: vesicle-mediated transport (2 terms)
• Biochemical function: structural molecule activity (2 terms)

DOI no: 10.1038/20708

Nature 399:371-375 (1999)

PubMed id: 10360576

Clathrin self-assembly is mediated by a tandemly repeated superhelix.

J.A.Ybe, F.M.Brodsky, K.Hofmann, K.Lin, S.H.Liu, L.Chen, T.N.Earnest, R.J.Fletterick, P.K.Hwang.

ABSTRACT

Clathrin is a triskelion-shaped cytoplasmic protein that polymerizes into a polyhedral lattice on intracellular membranes to form protein-coated membrane vesicles. Lattice formation induces the sorting of membrane proteins during endocytosis and organelle biogenesis by interacting with membrane-associated adaptor molecules. The clathrin triskelion is a trimer of heavy-chain subunits (1,675 residues), each binding a single light-chain subunit, in the hub domain (residues 1,074-1,675). Light chains negatively modulate polymerization so that intracellular clathrin assembly is adaptor-dependent. Here we report the atomic structure, to 2.6 A resolution, of hub residues 1,210-1,516 involved in mediating spontaneous clathrin heavy-chain polymerization and light-chain association. The hub fragment folds into an elongated coil of alpha-helices, and alignment analyses reveal a 145-residue motif that is repeated seven times along the filamentous leg and appears in other proteins involved in vacuolar protein sorting. The resulting model provides a three-dimensional framework for understanding clathrin heavy-chain self-assembly, light-chain binding and trimerization.

Selected figure(s)

Figure 2.
Figure 2: The crystal structure of clathrin heavy-chain residues 1,210–1,516. The two vertically aligned views are related by 90° rotation around the long axis of the protein. Images prepared wit BOBSCRIPT^28. a, Ribbon diagram, viewed on the helix face. Canonical helix hairpin unit is an N-terminal green helix joined to C-terminal yellow helix. Helices of each colour form a separate face or layer of parallel -helices. Hairpin turns form an 'edge' along the top. b, Cylinder representation, viewed on the hairpin edge, showing the relative orientation of individual helices, named as labelled. Side chain of Tyr 1,477 (red) is indicated. Grey cylinders represent helices 5c, 5d and 5e, identified in the electron-density map, but whose side chains could not be assigned. Red, green and blue bars delineate regions of CHCR5, CHCR6 and CHCR7, respectively. c, Topology diagram, indicating sequence boundaries of helices, labelled as in b.

Figure 5.
Figure 5: Surface representations of clathrin heavy chain, residues 1210–1516. Mappings of features onto the solvent-accessible surface were prepared with GRASP^29 and rendered using RASTER3D^30. Side chain of Tyr 1,477 (yellow–lime) is indicated in all panels. a, Surface electrostatic potential, with model oriented as in Fig. 2b. Red, negative charge; blue, positive charge. b, Distribution of muscle clathrin substitutions (purple/green), same view as a. Green substitutions (labelled) produce loss of side-chain charge. Blue represents neutral substitutions. c, Distribution of exposed hydrophobic regions (yellow) and exposed histidines (magenta). Helix-face view, with Tyr 1,477 towards viewer, rotated approximately 90° relative to a. Histidines of proximal leg, highly conserved among clathrins, tends to be exposed and positioned near loops and turns.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 399, 371-375) copyright 1999.

Figures were selected by an automated process.