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41  structures 1386  species 0  interactions 2667  sequences 30  architectures

Family: Clathrin_lg_ch (PF01086)

Summary: Clathrin light chain

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This is the Wikipedia entry entitled "Clathrin". More...

Clathrin Edit Wikipedia article

Clathrin is a protein that plays a major role in the formation of coated vesicles. Clathrin was first isolated and named by Barbara Pearse in 1976.[1] It forms a triskelion shape composed of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds the vesicle. This is how clathrin gets its name, from the Latin clathratus meaning like a lattice. Coat-proteins, like clathrin, are used to build small vesicles in order to transport molecules within cells. The endocytosis and exocytosis of vesicles allows cells to communicate, to transfer nutrients, to import signaling receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue inflammation. The endocytic pathway can be hijacked by viruses and other pathogens in order to gain entry to the cell during infection.[2]


Clathrin light chain a
NCBI gene1211
Other data
LocusChr. 9 q13
Clathrin light chain b
NCBI gene1212
Other data
LocusChr. 5 q35
A clathrin cage with a single triskelion highlighted in blue. CryoEM map EMD_5119 was rendered in UCSF Chimera and one clathrin triskelion was highlighted.
Clathrin heavy chain 1
Alt. symbolsCHC, CHC17, CLTCL2
NCBI gene1213
Other data
LocusChr. 17 q23.1-qter
Each cage has 12 pentagons. Mini-coat (left) has 4 hexagons and tetrahedral symmetry as in a truncated triakis tetrahedron. Hexagonal barrel (middle) has 8 hexagons and D6 symmetry. Soccer ball (right) has 20 hexagons and icosahedral symmetry as in a truncated icosahedron.
Mechanism of clathrin-mediated endocytosis.
Mechanism of clathrin-mediated endocytosis.
Clathrin heavy chain 2
Alt. symbolsCLTCL
NCBI gene8218
Other data
LocusChr. 22 q11.21
Clathrin propeller repeat
PDB 1c9l EBI.jpg
Clathrin terminal domain
Pfam clanCL0020
Clathrin heavy-chain linker
PDB 1b89 EBI.jpg
clathrin heavy chain repeat
Pfam clanCL0020

The clathrin triskelion is composed of three clathrin heavy chains interacting at their C-termini, each ~190 kDa heavy chain has a ~25 kDa light chain tightly bound to it. The three heavy chains provide the structural backbone of the clathrin lattice, and the three light chains are thought to regulate the formation and disassembly of a clathrin lattice. There are two forms of clathrin light chains, designated a and b. The main clathrin heavy chain, located on chromosome 17 in humans, is found in all cells. A second clathrin heavy chain gene, on chromosome 22, is expressed in muscle.

Clathrin heavy chain is often described as a leg, with subdomains, representing the foot (the N-terminal domain), followed by the ankle, distal leg, knee, proximal leg, and trimerization domains. The N-terminal domain consists of a seven-bladed β-propeller structure. The other domains form a super-helix of short alpha helices. This was originally determined from the structure of the proximal leg domain that identified and is composed of a smaller structural module referred to as clathrin heavy chain repeat motifs. The light chains bind primarily to the proximal leg portion of the heavy chain with some interaction near the trimerization domain. The β-propeller at the 'foot' of clathrin contains multiple binding sites for interaction with other proteins.

When triskelia assemble together in solution, they can interact with enough flexibility to form 6-sided rings (hexagons) that yield a flat lattice, or 5-sided rings (pentagons) that are necessary for curved lattice formation. When many triskelions connect, they can form a basket-like structure. The structure shown, is built of 36 triskelia, one of which is shown in blue. Another common assembly is a truncated icosahedron. To enclose a vesicle, exactly 12 pentagons must be present in the lattice.

In a cell, clathrin triskelion in the cytoplasm binds to an adaptor protein that has bound membrane, linking one of its three feet to the membrane at a time. Clathrin cannot bind to membrane or cargo directly and instead uses adaptor proteins to do this. This triskelion will bind to other membrane-attached triskelia to form a rounded lattice of hexagons and pentagons, reminiscent of the panels on a soccer ball, that pulls the membrane into a bud. By constructing different combinations of 5-sided and 6-sided rings, vesicles of different sizes may assemble. The smallest clathrin cage commonly imaged, called a mini-coat, has 12 pentagons and only two hexagons. Even smaller cages with zero hexagons probably do not form from the native protein, because the feet of the triskelia are too bulky.


Clathrin performs critical roles in shaping rounded vesicles in the cytoplasm for intracellular trafficking. Clathrin-coated vesicles (CCV) selectively sort cargo at the cell membrane, trans-Golgi network, and endosomal compartments for multiple membrane traffic pathways. After a vesicle buds into the cytoplasm, the coat rapidly disassembles, allowing the clathrin to recycle while the vesicle gets transported to a variety of locations.

Adaptor molecules are responsible for self-assembly and recruitment. Two examples of adaptor proteins are AP180[3] and epsin.[4][5][6] AP180 is used in synaptic vesicle formation. It recruits clathrin to membranes and also promotes its polymerization. Epsin also recruits clathrin to membranes and promotes its polymerization, and can help deform the membrane, and thus clathrin-coated vesicles can bud. In a cell, a triskelion floating in the cytoplasm binds to an adaptor protein, linking one of its feet to the membrane at a time. The skelion will bind to other ones attached to the membrane to form a polyhedral lattice, skelion, which pulls the membrane into a bud. The skelion does not bind directly to the membrane, but binds to the adaptor proteins that recognize the molecules on the membrane surface.

Clathrin has another function aside from the coating of organelles. In non-dividing cells, the formation of clathrin-coated vesicles occurs continuously. Formation of clathrin-coated vesicles is shut down in cells undergoing mitosis. During mitosis, clathrin binds to the spindle apparatus, in complex with two other proteins: TACC3 and ch-TOG/CKAP5. Clathrin aids in the congression of chromosomes by stabilizing kinetochore fibers of the mitotic spindle. The amino-terminal domain of the clathrin heavy chain and the TACC domain of TACC3 make the microtubule binding surface for TACC3/ch-TOG/clathrin to bind to the mitotic spindle. The stabilization of kinetochore fibers requires the trimeric structure of clathrin in order to crosslink microtubules.[7][8]

Clathrin-mediated endocytosis (CME) regulates many cellular physiological processes such as the internalization of growth factors and receptors, entry of pathogens, and synaptic transmission. It is believed that cellular invaders use the nutrient pathway to gain access to a cell's replicating mechanisms. Certain signalling molecules open the nutrients pathway. Two chemical compounds called Pitstop 1 and Pitstop 2, selective clathrin inhibitors, can interfere with the pathogenic activity, and thus protect the cells against invasion. These two compounds selectively block the endocytic ligand association with the clathrin terminal domain in vitro.[9] However, the specificity of these compounds to block clathrin-mediated endocytosis has been questioned.[10]

See also


  1. ^ Pearse BM (1976). "Clathrin: a unique protein associated with intracellular transfer of membrane by coated vesicles". Proceedings of the National Academy of Sciences of the United States of America. 73 (4): 1255–9. doi:10.1073/pnas.73.4.1255. PMC 430241. PMID 1063406.
  2. ^ "Archived copy". Archived from the original on 2016-01-16. Retrieved 2015-10-07.CS1 maint: archived copy as title (link)
  3. ^ McMahon HT. "Clathrin and its interactions with AP180". MRC Laboratory of Molecular Biology. Archived from the original on 2009-05-01. Retrieved 2009-04-17. micrographs of clathrin assembly
  4. ^ Ford MG, Pearse BM, Higgins MK, Vallis Y, Owen DJ, Gibson A, Hopkins CR, Evans PR, McMahon HT (February 2001). "Simultaneous binding of PtdIns(4,5)P2 and clathrin by AP180 in the nucleation of clathrin lattices on membranes" (PDF). Science. 291 (5506): 1051–5. CiteSeerX doi:10.1126/science.291.5506.1051. PMID 11161218. Archived from the original (PDF) on 2008-11-21. Retrieved 2009-04-17.
  5. ^ Higgins MK, McMahon HT (2002). "Snap-shots of clathrin-mediated endocytosis" (PDF). Trends in Biochemical Sciences. 27 (5): 257–63. doi:10.1016/S0968-0004(02)02089-3. PMID 12076538. Archived from the original (PDF) on 2008-11-21. Retrieved 2009-04-17.
  6. ^ Royle SJ, Bright NA, Lagnado L (2005). "Clathrin is required for the function of the mitotic spindle". Nature. 434 (7037): 1152–1157. doi:10.1038/nature03502. PMC 3492753. PMID 15858577.
  7. ^ Hood FE, Williams SJ, Burgess SG, Richards MW, Roth D, Straube A, Pfuhl M, Bayliss R, Royle SJ (2013). "Coordination of adjacent domains mediates TACC3-ch-TOG-clathrin assembly and mitotic spindle binding". Journal of Cell Biology. 202 (3): 463–78. doi:10.1083/jcb.201211127. PMC 3734082. PMID 23918938.
  8. ^ Role of the Clathrin Terminal Domain in Regulating Coated Pit Dynamics Revealed by Small Molecule Inhibition|Cell, Volume 146, Issue 3, 471-484, 5 August 2011 Abstract Archived 2012-01-19 at the Wayback Machine
  9. ^ Dutta D, Williamson CD, Cole NB, Donaldson JG (Sep 2012). "Pitstop 2 is a potent inhibitor of clathrin-independent endocytosis". PLoS ONE. 7 (9): e45799. doi:10.1371/journal.pone.0045799. PMC 3448704. PMID 23029248.

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This tab holds annotation information from the InterPro database.

InterPro entry IPR000996

Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport [ PUBMED:15261670 ]. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [ PUBMED:17449236 , PUBMED:11598180 ].

Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [ PUBMED:15752139 , PUBMED:16806884 ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase [ PUBMED:16734666 ]. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process [ PUBMED:15261670 ]. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins [ PUBMED:16699812 ].

This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains [ PUBMED:14617352 ]. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain.

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Seed source: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 81
Number in full: 2667
Average length of the domain: 204.10 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 82.32 %

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build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.8
Model length: 227
Family (HMM) version: 19
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Clathrin_lg_ch domain has been found. There are 41 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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