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PDBsum entry 1ky7

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Endocytosis/exocytosis PDB id
1ky7
Jmol
Contents
Protein chain
247 a.a. *
Ligands
SER-PHE-PHE-GLU-
ASP-ASN-PHE-VAL-
PRO
Waters ×162
* Residue conservation analysis
PDB id:
1ky7
Name: Endocytosis/exocytosis
Title: The ap-2 clathrin adaptor alpha-appendage in complex with amphiphysin fxdxf
Structure: Alpha-adaptin c. Chain: a. Fragment: c-terminal appendage (ear) residues 701-938. Synonym: ap-2 clathrin adaptor alpha subunit. Engineered: yes. Amphiphysin. Chain: p. Fragment: residues 322-330. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence is a naturally occuring sequence in amphiphysin (homo sapiens)
Biol. unit: Dimer (from PQS)
Resolution:
2.15Å     R-factor:   0.187     R-free:   0.252
Authors: T.J.Brett,L.M.Traub,D.H.Fremont
Key ref:
T.J.Brett et al. (2002). Accessory protein recruitment motifs in clathrin-mediated endocytosis. Structure, 10, 797-809. PubMed id: 12057195 DOI: 10.1016/S0969-2126(02)00784-0
Date:
03-Feb-02     Release date:   12-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17427  (AP2A2_MOUSE) -  AP-2 complex subunit alpha-2
Seq:
Struc:
 
Seq:
Struc:
938 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane coat   2 terms 
  Biological process     vesicle-mediated transport   2 terms 

 

 
DOI no: 10.1016/S0969-2126(02)00784-0 Structure 10:797-809 (2002)
PubMed id: 12057195  
 
 
Accessory protein recruitment motifs in clathrin-mediated endocytosis.
T.J.Brett, L.M.Traub, D.H.Fremont.
 
  ABSTRACT  
 
Clathrin-mediated endocytosis depends upon the interaction of accessory proteins with the alpha-ear of the AP-2 adaptor. We present structural characterization of these regulatory interactions. DPF and DPW motif peptides derived from eps15 and epsin bind in type I beta turn conformations to a conserved pocket on the alpha-ear platform. We show evidence for a second binding site that is DPW motif specific. The structure of a complex with an AP-2 binding segment from amphiphysin reveals a novel binding motif that we term FxDxF, which is engaged in an extended conformation by a unique surface of the platform domain. The FxDxF motif is also used by AP180 and the 170 kDa isoform of synaptojanin and can be found in several potential endocytic proteins, including HIP1, CD2AP, and PLAP. A mechanism of clathrin assembly regulation is suggested by three different AP-2 engagement modes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Experimental Evidence for DPF, DPW, and FxDxF Motif Peptides Binding to the a-Ear(A) Ribbon representation of the a-ear showing the binding sites of the FxDxF (extended platform site) and DPW2 (distal site) peptides, with the peptides shown as CPK models.(B-E) The fit of each peptide to its corresponding simulated annealing omit electron density contoured at 2.5 s.(B) The FxDxF peptide at 2.15 resolution.(C) The DPF peptide (in P2[1]) at 1.22 resolution.(D) The DPW1 peptide at 2.0 resolution.(E) The DPW2 peptide at 2.0 resolution. The orientation of the peptides depicted in B, C, and D were achieved by superposition of the a-ear platform domain. For the DPW2 peptide in (E), the Ca coordinates were aligned with those of the DPF peptide. DPF, cyan; DPW1, steel blue; DPW2, blue-green; FxDxF, magenta.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 797-809) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18182011 A.Harel, F.Wu, M.P.Mattson, C.M.Morris, and P.J.Yao (2008).
Evidence for CALM in Directing VAMP2 Trafficking.
  Traffic, 9, 417-429.  
18211691 C.J.DeRegis, P.B.Rahl, G.R.Hoffman, R.A.Cerione, and R.N.Collins (2008).
Mutational analysis of betaCOP (Sec26p) identifies an appendage domain critical for function.
  BMC Cell Biol, 9, 3.  
18068125 F.Buss, and J.Kendrick-Jones (2008).
How are the cellular functions of myosin VI regulated within the cell?
  Biochem Biophys Res Commun, 369, 165-175.  
17986441 L.E.Olesen, M.G.Ford, E.M.Schmid, Y.Vallis, M.M.Babu, P.H.Li, I.G.Mills, H.T.McMahon, and G.J.Praefcke (2008).
Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteins.
  J Biol Chem, 283, 5099-5109.
PDB code: 2vj0
18647389 L.Tomassi, A.Costantini, S.Corallino, E.Santonico, M.Carducci, G.Cesareni, and L.Castagnoli (2008).
The central proline rich region of POB1/REPS2 plays a regulatory role in epidermal growth factor receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteins.
  BMC Biochem, 9, 21.  
18354496 M.Sato, K.Sato, W.Liou, S.Pant, A.Harada, and B.D.Grant (2008).
Regulation of endocytic recycling by C. elegans Rab35 and its regulator RME-4, a coated-pit protein.
  EMBO J, 27, 1183-1196.  
18843039 P.A.Keyel, J.R.Thieman, R.Roth, E.Erkan, E.T.Everett, S.C.Watkins, J.E.Heuser, and L.M.Traub (2008).
The AP-2 adaptor beta2 appendage scaffolds alternate cargo endocytosis.
  Mol Biol Cell, 19, 5309-5326.  
18362180 R.I.Johnson, M.J.Seppa, and R.L.Cagan (2008).
The Drosophila CD2AP/CIN85 orthologue Cindr regulates junctions and cytoskeleton dynamics during tissue patterning.
  J Cell Biol, 180, 1191-1204.  
18772883 R.Mattera, and J.S.Bonifacino (2008).
Ubiquitin binding and conjugation regulate the recruitment of Rabex-5 to early endosomes.
  EMBO J, 27, 2484-2494.  
18165900 S.Símová, M.Klíma, L.Cermak, V.Sourková, and L.Andera (2008).
Arf and Rho GAP adapter protein ARAP1 participates in the mobilization of TRAIL-R1/DR4 to the plasma membrane.
  Apoptosis, 13, 423-436.  
17762867 B.Ritter, A.Y.Denisov, J.Philie, P.D.Allaire, V.Legendre-Guillemin, P.Zylbergold, K.Gehring, and P.S.McPherson (2007).
The NECAP PHear domain increases clathrin accessory protein binding potential.
  EMBO J, 26, 4066-4077.  
17631994 E.J.Ungewickell, and L.Hinrichsen (2007).
Endocytosis: clathrin-mediated membrane budding.
  Curr Opin Cell Biol, 19, 417-425.  
17187061 G.Spudich, M.V.Chibalina, J.S.Au, S.D.Arden, F.Buss, and J.Kendrick-Jones (2007).
Myosin VI targeting to clathrin-coated structures and dimerization is mediated by binding to Disabled-2 and PtdIns(4,5)P2.
  Nat Cell Biol, 9, 176-183.  
17257618 J.A.Ybe, S.Mishra, S.Helms, and J.Nix (2007).
Crystal structure at 2.8 A of the DLLRKN-containing coiled-coil domain of huntingtin-interacting protein 1 (HIP1) reveals a surface suitable for clathrin light chain binding.
  J Mol Biol, 367, 8.
PDB code: 2no2
17680766 M.L.Kuravsky, and V.I.Muronetz (2007).
Somatic and sperm-specific isoenzymes of glyceraldehyde-3-phosphate dehydrogenase: comparative analysis of primary structures and functional features.
  Biochemistry (Mosc), 72, 744-749.  
17052248 C.Knuehl, C.Y.Chen, V.Manalo, P.K.Hwang, N.Ota, and F.M.Brodsky (2006).
Novel binding sites on clathrin and adaptors regulate distinct aspects of coat assembly.
  Traffic, 7, 1688-1700.  
16493411 M.A.Edeling, C.Smith, and D.Owen (2006).
Life of a clathrin coat: insights from clathrin and AP structures.
  Nat Rev Mol Cell Biol, 7, 32-44.  
16945112 M.Döring, A.Loos, N.Schrader, B.Pfander, and R.Bauerfeind (2006).
Nerve growth factor-induced phosphorylation of amphiphysin-1 by casein kinase 2 regulates clathrin-amphiphysin interactions.
  J Neurochem, 98, 2013-2022.  
16497222 M.J.Hawryluk, P.A.Keyel, S.K.Mishra, S.C.Watkins, J.E.Heuser, and L.M.Traub (2006).
Epsin 1 is a polyubiquitin-selective clathrin-associated sorting protein.
  Traffic, 7, 262-281.  
16707503 S.Bruck, T.B.Huber, R.J.Ingham, K.Kim, H.Niederstrasser, P.M.Allen, T.Pawson, J.A.Cooper, and A.S.Shaw (2006).
Identification of a novel inhibitory actin-capping protein binding motif in CD2-associated protein.
  J Biol Chem, 281, 19196-19203.  
16837553 S.E.Dho, J.Trejo, D.P.Siderovski, and C.J.McGlade (2006).
Dynamic regulation of mammalian numb by G protein-coupled receptors and protein kinase C activation: Structural determinants of numb association with the cortical membrane.
  Mol Biol Cell, 17, 4142-4155.  
16806884 T.J.Brett, and L.M.Traub (2006).
Molecular structures of coat and coat-associated proteins: function follows form.
  Curr Opin Cell Biol, 18, 395-406.  
16415883 T.J.Brett, V.Legendre-Guillemin, P.S.McPherson, and D.H.Fremont (2006).
Structural definition of the F-actin-binding THATCH domain from HIP1R.
  Nat Struct Mol Biol, 13, 121-130.
PDB code: 1r0d
16262731 A.Meyerholz, L.Hinrichsen, S.Groos, P.C.Esk, G.Brandes, and E.J.Ungewickell (2005).
Effect of clathrin assembly lymphoid myeloid leukemia protein depletion on clathrin coat formation.
  Traffic, 6, 1225-1234.  
15752134 J.D.Mancias, and J.Goldberg (2005).
Exiting the endoplasmic reticulum.
  Traffic, 6, 278-285.  
15941406 J.Z.Rappoport, A.Benmerah, and S.M.Simon (2005).
Analysis of the AP-2 adaptor complex and cargo during clathrin-mediated endocytosis.
  Traffic, 6, 539-547.  
15800069 P.Monzo, N.C.Gauthier, F.Keslair, A.Loubat, C.M.Field, Y.Le Marchand-Brustel, and M.Cormont (2005).
Clues to CD2-associated protein involvement in cytokinesis.
  Mol Biol Cell, 16, 2891-2902.  
16231097 S.E.Holstein, and P.Oliviusson (2005).
Sequence analysis of Arabidopsis thaliana E/ANTH-domain-containing proteins: membrane tethers of the clathrin-dependent vesicle budding machinery.
  Protoplasma, 226, 13-21.  
15728179 S.K.Mishra, P.A.Keyel, M.A.Edeling, A.L.Dupin, D.J.Owen, and L.M.Traub (2005).
Functional dissection of an AP-2 beta2 appendage-binding sequence within the autosomal recessive hypercholesterolemia protein.
  J Biol Chem, 280, 19270-19280.  
14565955 A.Jha, N.R.Agostinelli, S.K.Mishra, P.A.Keyel, M.J.Hawryluk, and L.M.Traub (2004).
A novel AP-2 adaptor interaction motif initially identified in the long-splice isoform of synaptojanin 1, SJ170.
  J Biol Chem, 279, 2281-2290.  
15359277 B.Ritter, A.Y.Denisov, J.Philie, C.Deprez, E.C.Tung, K.Gehring, and P.S.McPherson (2004).
Two WXXF-based motifs in NECAPs define the specificity of accessory protein binding to AP-1 and AP-2.
  EMBO J, 23, 3701-3710.  
15473838 D.J.Owen, B.M.Collins, and P.R.Evans (2004).
Adaptors for clathrin coats: structure and function.
  Annu Rev Cell Dev Biol, 20, 153-191.  
15496985 G.J.Praefcke, M.G.Ford, E.M.Schmid, L.E.Olesen, J.L.Gallop, S.Y.Peak-Chew, Y.Vallis, M.M.Babu, I.G.Mills, and H.T.McMahon (2004).
Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosis.
  EMBO J, 23, 4371-4383.
PDB code: 1w80
15261670 H.T.McMahon, and I.G.Mills (2004).
COP and clathrin-coated vesicle budding: different pathways, common approaches.
  Curr Opin Cell Biol, 16, 379-391.  
14708007 J.S.Bonifacino (2004).
The GGA proteins: adaptors on the move.
  Nat Rev Mol Cell Biol, 5, 23-32.  
14690497 P.J.Watson, G.Frigerio, B.M.Collins, R.Duden, and D.J.Owen (2004).
Gamma-COP appendage domain - structure and function.
  Traffic, 5, 79-88.
PDB code: 1r4x
14665628 R.Mattera, B.Ritter, S.S.Sidhu, P.S.McPherson, and J.S.Bonifacino (2004).
Definition of the consensus motif recognized by gamma-adaptin ear domains.
  J Biol Chem, 279, 8018-8028.  
15292237 S.K.Mishra, M.J.Hawryluk, T.J.Brett, P.A.Keyel, A.L.Dupin, A.Jha, J.E.Heuser, D.H.Fremont, and L.M.Traub (2004).
Dual engagement regulation of protein interactions with the AP-2 adaptor alpha appendage.
  J Biol Chem, 279, 46191-46203.  
15520805 T.R.Dafforn, and C.J.Smith (2004).
Natively unfolded domains in endocytosis: hooks, lines and linkers.
  EMBO Rep, 5, 1046-1052.  
14679214 W.X.Schulze, and M.Mann (2004).
A novel proteomic screen for peptide-protein interactions.
  J Biol Chem, 279, 10756-10764.  
12858163 B.M.Collins, G.J.Praefcke, M.S.Robinson, and D.J.Owen (2003).
Structural basis for binding of accessory proteins by the appendage domain of GGAs.
  Nat Struct Biol, 10, 607-613.
PDB code: 1om9
14555962 B.Ritter, J.Philie, M.Girard, E.C.Tung, F.Blondeau, and P.S.McPherson (2003).
Identification of a family of endocytic proteins that define a new alpha-adaptin ear-binding motif.
  EMBO Rep, 4, 1089-1095.  
12886287 C.Knuehl, and F.M.Brodsky (2003).
The long and short of adaptor appendages.
  Nat Struct Biol, 10, 580-582.  
12858162 G.J.Miller, R.Mattera, J.S.Bonifacino, and J.H.Hurley (2003).
Recognition of accessory protein motifs by the gamma-adaptin ear domain of GGA3.
  Nat Struct Biol, 10, 599-606.
PDB code: 1p4u
14527408 G.R.Hoffman, P.B.Rahl, R.N.Collins, and R.A.Cerione (2003).
Conserved structural motifs in intracellular trafficking pathways: structure of the gammaCOP appendage domain.
  Mol Cell, 12, 615-625.
PDB code: 1pzd
12538641 I.G.Mills, G.J.Praefcke, Y.Vallis, B.J.Peter, L.E.Olesen, J.L.Gallop, P.J.Butler, P.R.Evans, and H.T.McMahon (2003).
EpsinR: an AP1/clathrin interacting protein involved in vesicle trafficking.
  J Cell Biol, 160, 213-222.  
12651740 J.S.Bonifacino, and L.M.Traub (2003).
Signals for sorting of transmembrane proteins to endosomes and lysosomes.
  Annu Rev Biochem, 72, 395-447.  
12892776 K.Farsad, and P.De Camilli (2003).
Mechanisms of membrane deformation.
  Curr Opin Cell Biol, 15, 372-381.  
14745135 K.Nakayama, and S.Wakatsuki (2003).
The structure and function of GGAs, the traffic controllers at the TGN sorting crossroads.
  Cell Struct Funct, 28, 431-442.  
12483220 M.C.Duncan, G.Costaguta, and G.S.Payne (2003).
Yeast epsin-related proteins required for Golgi-endosome traffic define a gamma-adaptin ear-binding motif.
  Nat Cell Biol, 5, 77-81.  
12742163 M.C.Duncan, and G.S.Payne (2003).
ENTH/ANTH domains expand to the Golgi.
  Trends Cell Biol, 13, 211-215.  
12505986 R.Mattera, C.N.Arighi, R.Lodge, M.Zerial, and J.S.Bonifacino (2003).
Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex.
  EMBO J, 22, 78-88.  
12578837 T.B.Huber, M.Schmidts, P.Gerke, B.Schermer, A.Zahn, B.Hartleben, L.Sellin, G.Walz, and T.Benzing (2003).
The carboxyl terminus of Neph family members binds to the PDZ domain protein zonula occludens-1.
  J Biol Chem, 278, 13417-13421.  
14504276 U.Andag, and H.D.Schmitt (2003).
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, 278, 51722-51734.  
12732633 U.Scheele, J.Alves, R.Frank, M.Duwel, C.Kalthoff, and E.Ungewickell (2003).
Molecular and functional characterization of clathrin- and AP-2-binding determinants within a disordered domain of auxilin.
  J Biol Chem, 278, 25357-25368.  
12461563 B.Wendland (2002).
Epsins: adaptors in endocytosis?
  Nat Rev Mol Cell Biol, 3, 971-977.  
12234931 S.K.Mishra, P.A.Keyel, M.J.Hawryluk, N.R.Agostinelli, S.C.Watkins, and L.M.Traub (2002).
Disabled-2 exhibits the properties of a cargo-selective endocytic clathrin adaptor.
  EMBO J, 21, 4915-4926.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.