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Scientists Determine Atomic Structure Of Lego-Like Molecule That Self-Assembles Into Cell's Cargo Capsule

University of California - San Francisco

The three-legged structure of the clathrin molecule (top), with the active site where adjacent molecules bind marked in yellow, and (bottom) close-up of the clathrin lattice formation.

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Scientists have determined the atomic structure of the three-spoked molecule called clathrin which "self-assembles," Lego-like, into a protective sphere just inside cell membranes and safely transports nutrients, hormones and other cargo into our cells.

The versatile molecule, which spontaneously disassembles and recycles after each delivery, was recently shown by other researchers to be targeted by the HIV virus. Invading viruses dupe clathrin into sequestering the cell's CD4 immune molecules, thereby preventing them from launching a defense against the virus. Knowledge of clathrin's atomic-level structure may enable researchers to counter the virus's pernicious strategy.

"If you know the structure, you can start understanding how clathrin is regulated," says Frances M. Brodsky, Ph.D., a leading clathrin researcher and a professor of biopharmaceutical sciences, pharmaceutical chemistry and microbiology and immunology at the University of California San Francisco (UCSF) where the study was carried out.

Brodsky and colleagues report the research in the May 27 issue of the journal Nature.

The atomic structure hints at what one of the UCSF scientists terms a "universal coupling motif" -- a configuration possibly shared by all proteins capable of coming together, like clathrin, and enclosing vital materiel in membranes for safe transit. Such controlled transport is essential for supplying nutrients and vitamins to cells, for secretion of hormones and for signaling cells to change their fate.

"Likely many proteins that contribute to traffic flow will have this motif," says Robert Fletterick, co-author on the Nature paper and a UCSF professor of biochemistry and biophysics. "Several have already been identified. The unmistakable footprint of the motif has just shown up in a protein involved in docking cells that are transported in membranous vessels in all animals and plants."

At the scale of the entire molecule, clathrin is shaped somewhat like a flattened tripod, and each three-legged structure is termed a triskelion. When precious proteins are to be hauled into the cell, clathrin molecules come together by the thousands and spontaneously assemble into a lattice, like a sheet of ice forming when the temperature drops. The clathrin lattice then folds into a ball.

"If you take a bunch of triskelions, they will self-assemble into a sphere," Brodsky says simply.

Formation of a clathrin-coated vesicle (from Essential Cell biology by Bruce Alberts, et. al.)

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The assembly is triggered when legs of adjacent clathrin triskelions pair up. As the assembly progresses, the triskelions form a growing network of hexagonal shapes. Ultimately, the flat lattice folds into a sphere made up of hexagonal shapes near the equator and clathrin pentagons near north and south poles, just like a soccerball.

The self-assembly not only assures safe transit for nutrients, hormones and the like, but also precisely regulates which molecules gain entry into the cell, and when: No clathrin, no entry.

When an iron-bearing protein, or insulin or the cholesterol molecule, for example, seek entry, each normally docks with a receptor protruding from the outer surface of the cell's membrane and specialized to accept only one kind of molecule. If the appropriate receptor -- say the receptor for insulin -- is not present, entry is barred.

But even when the insulin protein successfully links up with its receptor, the resulting insulin-receptor package must be recognized by another specialized cellular protein to gain entrance. This protein, known as an adaptor, acts as both bridge tender and bridge, binding to a specific receptor-cargo package on the outside the cell, and then to the clathrin molecule inside the cell membrane.

When triggered by the adaptor, the three-legged clathrin molecules line up with one another and begin the rapid polymerization into a lattice. The buildup pulls the adaptor and its receptor-cargo packet into the cell, eventually plucking a chunk of the cell's membrane inside, along with the receptor and its vital cargo. All this material becomes enveloped as the clathrin lattice folds into a sphere.

"The cell has figured out how to regulate the input of nutrients, hormones and other vital molecules," Brodsky says. "Central to that process is clathrin's capacity to first form a cage to transport its cargo, then disassemble, unload the cargo and finally recycle itself. It's a versatile molecule with a structure that determines its self-assembling and disassembling properties."

photomicrograph of formation of clatrhin-coated vesicle, with cell membrane beginning to be drawn inward at left, followed by clathrin lattice formation, formation of the sphere, and finally, completing process by pinching off the piece of cell membrane. (Also, from Alberts, crediting M.M. Perry and A.B. Gilbert, Cell Science 39:257-272.)

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The scientists discovered -- and report in Nature -- that most of the filamentous molecule is composed of seven repeats of five "helical hairpin" units. The helical hairpin is a common protein structure, but the repeating sequence of five may be unique to proteins involved in linking up to form coated vesicles for transport as clathrin does, says Robert Fletterick.

"The clathrin structure shows a gratifying elegance that would have delighted Bucky Fuller," he adds.

The researchers employed an advanced form of x-ray crystallography to determine the atomic structure of clathrin's active site of polymerization. The experiment made use of the Advanced Light Source at Lawrence Berkeley National Laboratory (LBNL).

Lead author of the paper is Joel A. Ybe, Ph.D., assistant research biochemist in the Brodsky laboratory. Senior author is Peter K. Hwang, Ph.D., associate research biochemisty in the UCSF biochemistry and biophysics department.

Other collaborators and co-authors are Kai Lin, Ph.D., former postdoctoral fellow in Fletterick's laboratory; Shu-Hui Liu, Ph.D., postdoctoral fellow and Lin Chen, research associate, both in Brodsky's lab. Also, Thomas N. Earnest, Ph.D., of the Macromolecular Crystallography Facility at LBL's Advanced Light Source, and Kay Hoffman, Ph.D., staff scientist at the Bioinformatics Group of MEMOREC in Germany.

The research was funded by the National Institutes of Health.


NOTE: Images of clathrin and its action inside cells can be viewed at

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