Table 1: Clathrin and COP coats: subunit functions and domains


AP1/GGA-associated proteins

AP2-associated proteins

COPI-associated proteins

COPII-associated proteins


Salient features

Peptide motifs





Endocytosis, sorting from TGN to endosomes, sorting from early to late endosomes

Heavy chain

Subunits polymerise into a triskelion; Atomic structures of several fragments reveal alpha-zigzag repeats and a beta-propeller terminal domain. [1, 2]

Binds LLDLD type 1 clathrin motif and PWxxW type 2 clathrin motif [3, 4].

Recognition of peptide motifs through the beta-propeller formed by WD40 repeats (terminal domain). Binding partners include auxilin, amphiphysin, epsin and AP180 [5-7]. The triskelial arms define skeleton of the clathrin coat.

Light chain: LCa/b

Interacts with Hsc70, calmodulin and the central helical/coiled coil domain of HIP1/HIP12 [8-11]


Regulates clathrin self-assembly into polyhedral lattices [12].

AP1 Adaptors



TGN-endosome sorting


Large AP complex subunit with truncated appendage domain [13]

Binds DFGx(bulky hydrophobic) and DFxDF motifs [14] [15].

Membrane binding via Arf1 [16].

Recruitment of accessory factors to AP1 complexes eg. EpsinR.



Clathrin box motif in hinge: LLNLD [17].

Binds dileucine cargo motifs:

[DE]xxxL[LI] [18].

Membrane binding via Arf1[19].

Binds to clathrin via hinge domain.

Binds accessory proteins via appendage domain.

Cargo recognition.

mu1 (A/B)


Binds Yxx(bulky hydrophobic) cargo motifs [20].

Cargo recognition.

Membrane interaction.


sigma1 sequence is weakly related to the N-terminal portion of mu.


Stabilises the AP core complex by mediating interactions between subunits [21].

AP2 adaptors



Plasma membrane endocytosis


Atomic structure of the appendage and trunk domain are known [22, 23].

Binds DxF,

FxDxF and

WVxF motifs [24-27]

Membrane binding.

Recruitment of accessory proteins eg. Epsin1 [28]


Atomic structure of the appendage and trunk domain are known [23, 29].

Clathrin box motif in hinge: LLNLD [30]. Binds cargo motif:

[DE]xxxL[LI] [31].

Binds to cargo dileucine motifs.

Binds clathrin via hinge domain.

Binds accessory proteins via appendage domain [32].


Atomic structure of m2 and of interactions with Yxx(bulky hydrophobic)

sorting motifs is known [33].

Binds Yxx(bulky hydrophobic) in cargo [20]

and WVxF in stonin 2 [34].

Membrane interaction.

Cargo recognition.

Also interacts with accessory proteins such as stonin 2.


sigma2 sequence is weakly related to N-terminal portion of mu.


Stabilises the AP core complex by mediating interactions between subunits.

AP3 adaptors[35, 36]



Melanosome biogenesis


Appendage domain and trunk domains conserved [36].


Like binds to accessory proteins via the appendage domain, but these have not been identified as yet [37].

beta3 (A/B)

Appendage domain and trunk domains conserved [38].

Clathrin box motif in hinge: LLDLD.

Binds cargo motif:

[DE]xxxL[LI] [39].

Binds clathrin.

Appendage domain with conserved ligand binding pocket likely binds to accessory proteins.

Cargo recognition

mu3 (A/B)


Binds cargo motif Yxx(bulky hydrophobic) [40].

Cargo recognition.

sigma3 (A/B)



Stabilises the AP3 complex.

AP4 adaptors [41-43]



Basolateral sorting/ TGN-endosome sorting




Membrane binding via Arf1.

Conserved appendage domain so likely recruits accessory proteins.



No obvious clathrin box

Binds the neuronal protein tyrosine phosphatases PTP-SL and PTPBR7 [44].

Has conserved appendage domain.



Binds Yxx(bulky hydrophobic) weakly and also interacts with other non-classical cargo motifs like DLYYDPM [45]

Cargo recognition.




Stabilises the AP4 complex.




TGN-endosome/lysosome sorting



Multidomain alternative adaptors with VHS, GAT, hinge and appendage domains.

Clathrin box motif in hinge: LLDDE.


Appendage domain binds DFGx(bulky hydrophobic) motifs[46, 47].


VHS domain binds

DxxLL motifs [48].


WNSF sequence in the hinge is bound by the AP1 gamma appendage [49].


Clathrin binding. Recruitment of accessory factors such as rabaptin-5 and p56 by appendage domain.

Cargo recognition (eg. Ci-M6PR) via VHS domain. Membrane recruitment via Arf binding to GAT domain[50].

Ubiquitin binding via GAT domain and thus potentially binds ubiquitinated cargo[51].



Clathrin box motifs in hinge: LIDLE and LLDLL. Other interactions are same as for GGA-1 [52].

Same as for GGA-1



Unidentified clathrin-binding motif and other interactions are same as for GGA-1 [53].

Same as for GGA-1


VHS, FYVE, Ubiquitin binding and clathrin binding.

FYVE domain binds to PtdIns(3)P.

Involved in flat clathrin lattice formation on early endosomes.


F-subcomplex: beta,delta,gamma,zeta[54]




Retrograde transport from the Golgi to the ER, maintenance of Golgi integrity


Small GTPase; Ras family


Recruitment of COPI coatomer to membranes in a GTP dependent manner [56].

alphaCOP / Ret1p

WD40 repeats (b-propeller domain) [57].

Binds KKxx, KxKxx motifs [58, 59].

Recruitment of cargo and accessory factors (eg Dsl1p).


Binds Arf1, and has weak sequence identity to b-adaptin.

Has appendage domain like large AP subunits.


Binds to diacidic cargo motifs [60].

Recruitment of cargo and accessory factors via appendage domain but these have not been identified.

Binds to KDEL receptor [61]

Beta-primeCOP / Sec26p

WD40 repeats (beta-propeller) [57]

Binds KxKxx motif.

Recruitment of cargo.

gammaCOP / Sec21p

Binds members of the p24 family [62].

Has appendage domain like large AP subunits [63, 64].


Recruitment of cargo.

Recruitment of cargo and accessory factors (ArfGAP) via appendage domain.

deltaCOP / Ret2p

Weak sequence identity to mu-adaptin.

Binds WxxxW motif in the acidic domain of Dsl1p [65, 66].

Binds accessory protein via acidic tryptophan motif.

epsilonCOP / Sec28p



May stabilise the complex in that point mutations are often lethal in yeast [67].

zetaCOP / Ret3p

Weak sequence identity to sigma-adaptin [68].


Stabilises the interaction between beta-COP and gamma-COP.


GTPase activating protein for ARF[69].

Binds beta-prime WD40 domain and gamma-COP appendage domain.


Activates Arf GTP hydrolysis to promote coat disassembly.

Complexes with the KDEL receptor [61]

ARFGEFs Gea1p/Gea2p

GEF for ARF [70, 71]






Protein export from the ER


Small GTPase of the Ras family [72].


Recruits coat components to membranes in a GTP dependent manner[73].



Both subunits have WD40 repeats (beta-propeller domains)[72, 74].

Not identified as yet

Induces coat polymerisation.


Sec23 is a Sar1p GTPase activating protein and Sec24 binds cargo [75]

Sec24 binds DxE,


Lxx[L/M]E motifs [75-77].

Has GAP activity for Sar1p,

Cargo recognition

and membrane curvature selection.


Has a GEF domain.


ER localised GEF and thus leads to the recruitment of Sar1p and COPII coat components to the ER [78].


Forms a ternary complex with Sec23/24p in vitro [79]


Stabilizes Sec23/24 complex and stimulates vesicle budding [80]






1.         Smith, C.J. and B.M. Pearse, Clathrin: anatomy of a coat protein. Trends Cell Biol, 1999. 9(9): p. 335-8.

2.         ter Haar, E., et al., Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker. Cell, 1998. 95(4): p. 563-73.

3.         Miele, A.E., et al., Two distinct interaction motifs in amphiphysin bind two independent sites on the clathrin terminal domain beta-propeller. Nat Struct Mol Biol, 2004. 11(3): p. 242-8.

4.         Drake, M.T. and L.M. Traub, Interaction of two structurally distinct sequence types with the clathrin terminal domain beta-propeller. J Biol Chem, 2001. 276(31): p. 28700-9.

5.         Ford, M.G., et al., Simultaneous binding of PtdIns(4,5)P2 and clathrin by AP180 in the nucleation of clathrin lattices on membranes. Science, 2001. 291(5506): p. 1051-5.

6.         Scheele, U., et al., Molecular and functional characterization of clathrin- and AP-2-binding determinants within a disordered domain of auxilin. J Biol Chem, 2003. 278(28): p. 25357-68.

7.         Smith, C.J., et al., Location of auxilin within a clathrin cage. J Mol Biol, 2004. 336(2): p. 461-71.

8.         Pley, U.M., et al., The interaction of calmodulin with clathrin-coated vesicles, triskelions, and light chains. Localization of a binding site. J Biol Chem, 1995. 270(5): p. 2395-402.

9.         Nathke, I., et al., The calcium-binding site of clathrin light chains. J Biol Chem, 1990. 265(30): p. 18621-7.

10.       DeLuca-Flaherty, C., et al., Uncoating protein (hsc70) binds a conformationally labile domain of clathrin light chain LCa to stimulate ATP hydrolysis. Cell, 1990. 62(5): p. 875-87.

11.       Legendre-Guillemin, V., et al., HIP1 and HIP12 display differential binding to F-actin, AP2, and clathrin. Identification of a novel interaction with clathrin light chain. J Biol Chem, 2002. 277(22): p. 19897-904.

12.       Ybe, J.A., et al., Clathrin self-assembly is regulated by three light-chain residues controlling the formation of critical salt bridges. Embo J, 1998. 17(5): p. 1297-303.

13.       Kent, H.M., et al., Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin. Structure (Camb), 2002. 10(8): p. 1139-48.

14.       Shiba, Y., et al., Gamma-adaptin interacts directly with Rabaptin-5 through its ear domain. J Biochem (Tokyo), 2002. 131(3): p. 327-36.

15.       Hirst, J., et al., EpsinR: an ENTH domain-containing protein that interacts with AP-1. Mol Biol Cell, 2003. 14(2): p. 625-41.

16.       Traub, L.M., J.A. Ostrom, and S. Kornfeld, Biochemical dissection of AP-1 recruitment onto Golgi membranes. J Cell Biol, 1993. 123(3): p. 561-73.

17.       Doray, B. and S. Kornfeld, Gamma subunit of the AP-1 adaptor complex binds clathrin: implications for cooperative binding in coated vesicle assembly. Mol Biol Cell, 2001. 12(7): p. 1925-35.

18.       Rapoport, I., et al., Dileucine-based sorting signals bind to the beta chain of AP-1 at a site distinct and regulated differently from the tyrosine-based motif-binding site. Embo J, 1998. 17(8): p. 2148-55.

19.       Austin, C., I. Hinners, and S.A. Tooze, Direct and GTP-dependent interaction of ADP-ribosylation factor 1 with clathrin adaptor protein AP-1 on immature secretory granules. J Biol Chem, 2000. 275(29): p. 21862-9.

20.       Ohno, H., et al., Interaction of tyrosine-based sorting signals with clathrin-associated proteins. Science, 1995. 269(5232): p. 1872-5.

21.       Takatsu, H., et al., Similar subunit interactions contribute to assembly of clathrin adaptor complexes and COPI complex: analysis using yeast three-hybrid system. Biochem Biophys Res Commun, 2001. 284(4): p. 1083-9.

22.       Owen, D.J., et al., A structural explanation for the binding of multiple ligands by the alpha-adaptin appendage domain. Cell, 1999. 97(6): p. 805-15.

23.       Collins, B.M., et al., Molecular architecture and functional model of the endocytic AP2 complex. Cell, 2002. 109(4): p. 523-35.

24.       Brett, T.J., L.M. Traub, and D.H. Fremont, Accessory protein recruitment motifs in clathrin-mediated endocytosis. Structure (Camb), 2002. 10(6): p. 797-809.

25.       Jha, A., et al., A novel AP-2 adaptor interaction motif initially identified in the long-splice isoform of synaptojanin 1, SJ170. J Biol Chem, 2004. 279(3): p. 2281-90.

26.       Walther, K., et al., Functional dissection of the interactions of stonin 2 with the adaptor complex AP-2 and synaptotagmin, in Proc Natl Acad Sci U S A. 2004. p. 964-9.

27.       Benmerah, A., et al., The ear of alpha-adaptin interacts with the COOH-terminal domain of the Eps 15 protein. J Biol Chem, 1996. 271(20): p. 12111-6.

28.       Chen, H., et al., Epsin is an EH-domain-binding protein implicated in clathrin-mediated endocytosis. Nature, 1998. 394(6695): p. 793-7.

29.       Owen, D.J., et al., The structure and function of the beta 2-adaptin appendage domain. Embo J, 2000. 19(16): p. 4216-27.

30.       Shih, W., A. Gallusser, and T. Kirchhausen, A clathrin-binding site in the hinge of the beta 2 chain of mammalian AP-2 complexes. J Biol Chem, 1995. 270(52): p. 31083-90.

31.       Hofmann, M.W., et al., The leucine-based sorting motifs in the cytoplasmic domain of the invariant chain are recognized by the clathrin adaptors AP1 and AP2 and their medium chains. J Biol Chem, 1999. 274(51): p. 36153-8.

32.       Owen, D.J., et al., The structure and function of the beta 2-adaptin appendage domain, in Embo J. 2000. p. 4216-27.

33.       Owen, D.J. and P.R. Evans, A structural explanation for the recognition of tyrosine-based endocytotic signals. Science, 1998. 282(5392): p. 1327-32.

34.       Walther, K., et al., Functional dissection of the interactions of stonin 2 with the adaptor complex AP-2 and synaptotagmin. Proc Natl Acad Sci U S A, 2004. 101(4): p. 964-9.

35.       Mullins, C., L.M. Hartnell, and J.S. Bonifacino, Distinct requirements for the AP-3 adaptor complex in pigment granule and synaptic vesicle biogenesis in Drosophila melanogaster. Mol Gen Genet, 2000. 263(6): p. 1003-14.

36.       Simpson, F., et al., Characterization of the adaptor-related protein complex, AP-3. J Cell Biol, 1997. 137(4): p. 835-45.

37.       Suzuki, T., et al., Evaluation of the delta subunit of bovine adaptor protein complex 3 as a receptor for bovine leukaemia virus. J Gen Virol, 2003. 84(Pt 5): p. 1309-16.

38.       Dell'Angelica, E.C., C.E. Ooi, and J.S. Bonifacino, Beta3A-adaptin, a subunit of the adaptor-like complex AP-3. J Biol Chem, 1997. 272(24): p. 15078-84.

39.       Craig, H.M., et al., Interactions of HIV-1 nef with the mu subunits of adaptor protein complexes 1, 2, and 3: role of the dileucine-based sorting motif. Virology, 2000. 271(1): p. 9-17.

40.       Dell'Angelica, E.C., et al., AP-3: an adaptor-like protein complex with ubiquitous expression. Embo J, 1997. 16(5): p. 917-28.

41.       Dell'Angelica, E.C., C. Mullins, and J.S. Bonifacino, AP-4, a novel protein complex related to clathrin adaptors. J Biol Chem, 1999. 274(11): p. 7278-85.

42.       Dell'Angelica, E.C., C. Mullins, and J.S. Bonifacino, AP-4, a novel protein complex related to clathrin adaptors, in J Biol Chem. 1999. p. 7278-85.

43.       Hirst, J., et al., Characterization of a fourth adaptor-related protein complex. Mol Biol Cell, 1999. 10(8): p. 2787-802.

44.       Dilaver, G., et al., Colocalisation of the protein tyrosine phosphatases PTP-SL and PTPBR7 with beta4-adaptin in neuronal cells. Histochem Cell Biol, 2003. 119(1): p. 1-13.

45.       Aguilar, R.C., et al., Signal-binding specificity of the mu4 subunit of the adaptor protein complex AP-4. J Biol Chem, 2001. 276(16): p. 13145-52.

46.       Mattera, R., et al., Definition of the Consensus Motif Recognized by {gamma}-Adaptin Ear Domains. J Biol Chem, 2004. 279(9): p. 8018-8028.

47.       Mattera, R., et al., Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex. Embo J, 2003. 22(1): p. 78-88.

48.       Shiba, T., et al., Structural basis for recognition of acidic-cluster dileucine sequence by GGA1. Nature, 2002. 415(6874): p. 937-41.

49.       Bai, H., B. Doray, and S. Kornfeld, GGA1 interacts with the adaptor protein AP-1 through a WNSF sequence in its hinge region. J Biol Chem, 2004.

50.       Collins, B.M., P.J. Watson, and D.J. Owen, The structure of the GGA1-GAT domain reveals the molecular basis for ARF binding and membrane association of GGAs. Dev Cell, 2003. 4(3): p. 321-32.

51.       Shiba, Y., et al., GAT (GGA and Tom1) Domain Responsible for Ubiquitin Binding and Ubiquitination. J Biol Chem, 2004. 279(8): p. 7105-7111.

52.       Ghosh, P., et al., Mammalian GGAs act together to sort mannose 6-phosphate receptors. J Cell Biol, 2003. 163(4): p. 755-66.

53.       Miller, G.J., et al., Recognition of accessory protein motifs by the gamma-adaptin ear domain of GGA3. Nat Struct Biol, 2003. 10(8): p. 599-606.

54.       Schledzewski, K., H. Brinkmann, and R.R. Mendel, Phylogenetic analysis of components of the eukaryotic vesicle transport system reveals a common origin of adaptor protein complexes 1, 2, and 3 and the F subcomplex of the coatomer COPI. J Mol Evol, 1999. 48(6): p. 770-8.

55.       Takatsu, H., et al., Similar subunit interactions contribute to assembly of clathrin adaptor complexes and COPI complex: analysis using yeast three-hybrid system, in Biochem Biophys Res Commun. 2001. p. 1083-9.

56.       Liang, J.O. and S. Kornfeld, Comparative activity of ADP-ribosylation factor family members in the early steps of coated vesicle formation on rat liver Golgi membranes. J Biol Chem, 1997. 272(7): p. 4141-8.

57.       Eugster, A., et al., The {alpha}- and {beta}'-COP WD40 domains mediate cargo-selective interactions with distinct di-lysine motifs. Mol Biol Cell, 2003.

58.       Cosson, P., et al., New COP1-binding motifs involved in ER retrieval. Embo J, 1998. 17(23): p. 6863-70.

59.       Rohde, H.M., et al., The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex. J Biol Chem, 2003. 278(52): p. 52689-99.

60.       Piguet, V., et al., Nef-induced CD4 degradation: a diacidic-based motif in Nef functions as a lysosomal targeting signal through the binding of beta-COP in endosomes. Cell, 1999. 97(1): p. 63-73.

61.       Majoul, I., et al., KDEL-cargo regulates interactions between proteins involved in COPI vesicle traffic: measurements in living cells using FRET. Dev Cell, 2001. 1(1): p. 139-53.

62.       Fiedler, K., et al., Bimodal interaction of coatomer with the p24 family of putative cargo receptors. Science, 1996. 273(5280): p. 1396-9.

63.       Watson, P.J., et al., Gamma-COP appendage domain - structure and function. Traffic, 2004. 5(2): p. 79-88.

64.       Hoffman, G.R., et al., Conserved structural motifs in intracellular trafficking pathways: structure of the gammaCOP appendage domain. Mol Cell, 2003. 12(3): p. 615-25.

65.       Andag, U., T. Neumann, and H.D. Schmitt, The coatomer-interacting protein Dsl1p is required for Golgi-to-endoplasmic reticulum retrieval in yeast. J Biol Chem, 2001. 276(42): p. 39150-60.

66.       Andag, U. and H.D. Schmitt, Dsl1p, an essential component of the Golgi-endoplasmic reticulum retrieval system in yeast, uses the same sequence motif to interact with different subunits of the COPI vesicle coat. J Biol Chem, 2003. 278(51): p. 51722-34.

67.       Duden, R., et al., epsilon-COP is a structural component of coatomer that functions to stabilize alpha-COP. Embo J, 1998. 17(4): p. 985-95.

68.       Cosson, P., et al., Delta- and zeta-COP, two coatomer subunits homologous to clathrin-associated proteins, are involved in ER retrieval. Embo J, 1996. 15(8): p. 1792-8.

69.       Dogic, D., et al., The ADP-ribosylation factor GTPase-activating protein Glo3p is involved in ER retrieval. Eur J Cell Biol, 1999. 78(5): p. 305-10.

70.       Peyroche, A., et al., The ARF exchange factors Gea1p and Gea2p regulate Golgi structure and function in yeast. J Cell Sci, 2001. 114(Pt 12): p. 2241-53.

71.       Spang, A., et al., The ADP ribosylation factor-nucleotide exchange factors Gea1p and Gea2p have overlapping, but not redundant functions in retrograde transport from the Golgi to the endoplasmic reticulum. Mol Biol Cell, 2001. 12(4): p. 1035-45.

72.       Salama, N.R., J.S. Chuang, and R.W. Schekman, Sec31 encodes an essential component of the COPII coat required for transport vesicle budding from the endoplasmic reticulum. Mol Biol Cell, 1997. 8(2): p. 205-17.

73.       Barlowe, C., et al., COPII: a membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum. Cell, 1994. 77(6): p. 895-907.

74.       Swaroop, A., et al., Molecular characterization of a novel human gene, SEC13R, related to the yeast secretory pathway gene SEC13, and mapping to a conserved linkage group on human chromosome 3p24-p25 and mouse chromosome 6. Hum Mol Genet, 1994. 3(8): p. 1281-6.

75.       Bi, X., R.A. Corpina, and J. Goldberg, Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat. Nature, 2002. 419(6904): p. 271-7.

76.       Miller, E.A., et al., Multiple cargo binding sites on the COPII subunit Sec24p ensure capture of diverse membrane proteins into transport vesicles. Cell, 2003. 114(4): p. 497-509.

77.       Barlowe, C., Molecular recognition of cargo by the COPII complex: a most accommodating coat. Cell, 2003. 114(4): p. 395-7.

78.       Weissman, J.T., H. Plutner, and W.E. Balch, The mammalian guanine nucleotide exchange factor mSec12 is essential for activation of the Sar1 GTPase directing endoplasmic reticulum export. Traffic, 2001. 2(7): p. 465-75.

79.       Gimeno, R.E., P. Espenshade, and C.A. Kaiser, COPII coat subunit interactions: Sec24p and Sec23p bind to adjacent regions of Sec16p. Mol Biol Cell, 1996. 7(11): p. 1815-23.

80.       Supek, F., et al., Sec16p potentiates the action of COPII proteins to bud transport vesicles. J Cell Biol, 2002. 158(6): p. 1029-38.