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Endocytosis/exocytosis PDB id
1xi5
Jmol
Contents
Protein chains
(+ 3 more) 1630 a.a.* *
(+ 3 more) 114 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1xi5
Name: Endocytosis/exocytosis
Title: Clathrin d6 coat with auxilin j-domain
Structure: Clathrin heavy chain. Chain: a, b, c, d, e, f, g, h, i. Fragment: residues 1-1630. Auxilin j-domain. Chain: j, k, l, m, n, o, p, q, r. Fragment: residues 797-910
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: brain. Tissue: brain
Authors: A.Fotin,Y.Cheng,N.Grigorieff,T.Walz,S.C.Harrison,T.Kirchhaus
Key ref:
A.Fotin et al. (2004). Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Nature, 432, 649-653. PubMed id: 15502813 DOI: 10.1038/nature03078
Date:
21-Sep-04     Release date:   02-Nov-04    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P49951  (CLH1_BOVIN) -  Clathrin heavy chain 1
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1675 a.a.
1630 a.a.
Protein chains
Pfam   ArchSchema ?
Q27974  (AUXI_BOVIN) -  Putative tyrosine-protein phosphatase auxilin
Seq:
Struc: 		 
Seq:
Struc: 		910 a.a.
114 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains J, K, L, M, N, O, P, Q, R: E.C.3.1.3.48  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
 + H(2)O
 = protein tyrosine
 + phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     vesicle-mediated transport   2 terms 
  Biochemical function     structural molecule activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature03078 Nature 432:649-653 (2004)
PubMed id: 15502813  
 
 
Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating.
A.Fotin, Y.Cheng, N.Grigorieff, T.Walz, S.C.Harrison, T.Kirchhausen.
 
  ABSTRACT  
 
Clathrin-coated pits invaginate from specific membrane compartments and pinch off as coated vesicles. These vesicles then uncoat rapidly once released. The Hsc70 molecular chaperone effects the uncoating reaction, and is guided to appropriate locations on clathrin lattices by the J-domain-containing co-chaperone molecule auxilin. This raises the question of how a local event such as ATP hydrolysis by Hsc70 can catalyse a global disassembly. Here, we have used electron cryomicroscopy to determine 12-A-resolution structures of in-vitro-assembled clathrin coats in association with a carboxy-terminal fragment of auxilin that contains both the clathrin-binding region and the J domain. We have located the auxilin fragment by computing differences between these structures and those lacking auxilin (described in an accompanying paper). Auxilin binds within the clathrin lattice near contacts between an inward-projecting C-terminal helical tripod and the crossing of two 'ankle' segments; it also contacts the terminal domain of yet another clathrin 'leg'. It therefore recruits Hsc70 to the neighbourhood of a set of critical interactions. Auxilin binding produces a local change in heavy-chain contacts, creating a detectable global distortion of the clathrin coat. We propose a mechanism by which local destabilization of the lattice promotes general uncoating.
 
  Selected figure(s)  
 
Figure 3.
Figure 3: Changes in clathrin heavy-chain contacts produced by auxilin binding. a, Comparison of the arrangement of clathrin legs in the region around a vertex of the D6 barrel (the "hub assembly", as defined in the accompanying paper5). The model from our 7.9 Å resolution analysis of a D6 barrel is in blue; the one obtained by adjusting that model to fit the 12 Å auxilin-bound D6 barrel is in red. The ankle-crossing angles change in such a way that the terminal domains move radially outwards with respect to the outer shell. b, Superposition of clathrin triskelions from corresponding locations in the auxilin-bound D6 barrel (red) and the auxilin-free D6 barrel (blue). 		Figure 4.
Figure 4: Fit of the auxilin J domain into the difference density. a, Auxilin difference density in relation to the hub assembly model. The view is the same as in Fig. 3a. A terminal-domain linker segment projecting towards this hub from another heavy chain centred three vertices away is in gold. The auxilin fragment fits into the intersection of the crossed ankles and also contacts the terminal domain emanating from a different hub. b, c, Different views showing the fit of the solution structure of the C-terminal, 110-residue fragment of bovine auxilin obtained by NMR12 into the electron density map. Blue indicates the region of auxilin proposed to contact Hsc70 (ref. 11).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 432, 649-653) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482805 A.Rothnie, A.R.Clarke, P.Kuzmic, A.Cameron, and C.J.Smith (2011).
A sequential mechanism for clathrin cage disassembly by 70-kDa heat-shock cognate protein (Hsc70) and auxilin.
  Proc Natl Acad Sci U S A, 108, 6927-6932.  
21278753 T.Böcking, F.Aguet, S.C.Harrison, and T.Kirchhausen (2011).
Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating.
  Nat Struct Mol Biol, 18, 295-301.  
20486136 J.Pizarro-Cerdá, M.Bonazzi, and P.Cossart (2010).
Clathrin-mediated endocytosis: what works for small, also works for big.
  Bioessays, 32, 496-504.  
20826345 R.Guan, H.Dai, D.Han, S.C.Harrison, and T.Kirchhausen (2010).
Structure of the PTEN-like region of auxilin, a detector of clathrin-coated vesicle budding.
  Structure, 18, 1191-1198.
PDB code: 3n0a
20150955 S.Zeng, H.Liu, and Q.Yang (2010).
Application of symmetry adapted function method for three-dimensional reconstruction of octahedral biological macromolecules.
  Int J Biomed Imaging, 2010, 195274.  
20033059 Y.Xing, T.Böcking, M.Wolf, N.Grigorieff, T.Kirchhausen, and S.C.Harrison (2010).
Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly.
  EMBO J, 29, 655-665.  
19296488 S.Mostowy, and P.Cossart (2009).
Cytoskeleton rearrangements during Listeria infection: clathrin and septins as new players in the game.
  Cell Motil Cytoskeleton, 66, 816-823.  
19809571 S.Saffarian, E.Cocucci, and T.Kirchhausen (2009).
Distinct dynamics of endocytic clathrin-coated pits and coated plaques.
  PLoS Biol, 7, e1000191.  
19536138 Y.Mao, D.M.Balkin, R.Zoncu, K.S.Erdmann, L.Tomasini, F.Hu, M.M.Jin, M.E.Hodsdon, and P.De Camilli (2009).
A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism.
  EMBO J, 28, 1831-1842.
PDB codes: 2kie 2kig
17978091 I.Rapoport, W.Boll, A.Yu, T.Böcking, and T.Kirchhausen (2008).
A motif in the clathrin heavy chain required for the hsc70/auxilin uncoating reaction.
  Mol Biol Cell, 19, 405-413.  
17921208 S.Schein, M.Sands-Kidner, and T.Friedrich (2008).
The physical basis for the head-to-tail rule that excludes most fullerene cages from self-assembly.
  Biophys J, 94, 938-957.  
17921209 S.Schein, and M.Sands-Kidner (2008).
A geometric principle may guide self-assembly of fullerene cages from clathrin triskelia and from carbon atoms.
  Biophys J, 94, 958-976.  
17702618 A.Young (2007).
Structural insights into the clathrin coat.
  Semin Cell Dev Biol, 18, 448-458.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
17116403 C.Xiao, and M.G.Rossmann (2007).
Interpretation of electron density with stereographic roadmap projections.
  J Struct Biol, 158, 182-187.  
17652132 E.Demoinet, A.Jacquier, G.Lutfalla, and M.Fromont-Racine (2007).
The Hsp40 chaperone Jjj1 is required for the nucleo-cytoplasmic recycling of preribosomal factors in Saccharomyces cerevisiae.
  RNA, 13, 1570-1581.  
17488288 E.Eisenberg, and L.E.Greene (2007).
Multiple roles of auxilin and hsc70 in clathrin-mediated endocytosis.
  Traffic, 8, 640-646.  
17804463 M.Stahl, M.Retzlaff, M.Nassal, and J.Beck (2007).
Chaperone activation of the hepadnaviral reverse transcriptase for template RNA binding is established by the Hsp70 and stimulated by the Hsp90 system.
  Nucleic Acids Res, 35, 6124-6136.  
17604721 S.Fath, J.D.Mancias, X.Bi, and J.Goldberg (2007).
Structure and organization of coat proteins in the COPII cage.
  Cell, 129, 1325-1336.
PDB codes: 2pm6 2pm7 2pm9
17395454 S.M.Stagg, P.LaPointe, and W.E.Balch (2007).
Structural design of cage and coat scaffolds that direct membrane traffic.
  Curr Opin Struct Biol, 17, 221-228.  
17095010 Y.Cheng, W.Boll, T.Kirchhausen, S.C.Harrison, and T.Walz (2007).
Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.
  J Mol Biol, 365, 892-899.  
16962776 E.Veiga, and P.Cossart (2006).
The role of clathrin-dependent endocytosis in bacterial internalization.
  Trends Cell Biol, 16, 499-504.  
16687570 J.Xiao, L.S.Kim, and T.R.Graham (2006).
Dissection of Swa2p/auxilin domain requirements for cochaperoning Hsp70 clathrin-uncoating activity in vivo.
  Mol Biol Cell, 17, 3281-3290.  
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.  
16501097 M.R.Auerbach, K.R.Brown, A.Kaplan, D.de Las Nueces, and I.R.Singh (2006).
A small loop in the capsid protein of Moloney murine leukemia virus controls assembly of spherical cores.
  J Virol, 80, 2884-2893.  
16798879 R.H.Massol, W.Boll, A.M.Griffin, and T.Kirchhausen (2006).
A burst of auxilin recruitment determines the onset of clathrin-coated vesicle uncoating.
  Proc Natl Acad Sci U S A, 103, 10265-10270.  
17026666 R.Sousa, and E.M.Lafer (2006).
Keep the traffic moving: mechanism of the Hsp70 motor.
  Traffic, 7, 1596-1603.  
16571680 W.Natsume, K.Tanabe, S.Kon, N.Yoshida, T.Watanabe, T.Torii, and M.Satake (2006).
SMAP2, a novel ARF GTPase-activating protein, interacts with clathrin and clathrin assembly protein and functions on the AP-1-positive early endosome/trans-Golgi network.
  Mol Biol Cell, 17, 2592-2603.  
15596443 J.B.Heymann, K.Iwasaki, Y.I.Yim, N.Cheng, D.M.Belnap, L.E.Greene, E.Eisenberg, and A.C.Steven (2005).
Visualization of the binding of Hsc70 ATPase to clathrin baskets: implications for an uncoating mechanism.
  J Biol Chem, 280, 7156-7161.  
15752134 J.D.Mancias, and J.Goldberg (2005).
Exiting the endoplasmic reticulum.
  Traffic, 6, 278-285.  
15752139 J.D.Wilbur, P.K.Hwang, and F.M.Brodsky (2005).
New faces of the familiar clathrin lattice.
  Traffic, 6, 346-350.  
16179350 M.Girard, V.Poupon, F.Blondeau, and P.S.McPherson (2005).
The DnaJ-domain protein RME-8 functions in endosomal trafficking.
  J Biol Chem, 280, 40135-40143.  
15766537 W.Chiu, M.L.Baker, W.Jiang, M.Dougherty, and M.F.Schmid (2005).
Electron cryomicroscopy of biological machines at subnanometer resolution.
  Structure, 13, 363-372.  
15577897 F.M.Brodsky (2004).
Cell biology: clathrin's Achilles' ankle.
  Nature, 432, 568-569.  
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.