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PDBsum entry 2v6x

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protein ligands Protein-protein interface(s) links
Protein transport PDB id
2v6x
Jmol
Contents
Protein chains
82 a.a. *
41 a.a. *
Ligands
SO4
Waters ×32
* Residue conservation analysis
PDB id:
2v6x
Name: Protein transport
Title: Stractural insight into the interaction between escrt-iii and vps4
Structure: Vacuolar protein sorting-associated protein 4. Chain: a. Fragment: mit domain resiudes 1-82. Synonym: vps4, protein end13, doa4-independent degradation 6, vacuolar protein-targeting protein 10. Engineered: yes. Doa4-independent degradation protein 4. Chain: b. Fragment: c-terminal fragment residues 102-151.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.98Å     R-factor:   0.200     R-free:   0.228
Authors: T.Obita,O.Perisic,S.Ghazi-Tabatabai,S.Saksena,S.D.Emr, R.L.W
Key ref:
T.Obita et al. (2007). Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4. Nature, 449, 735-739. PubMed id: 17928861 DOI: 10.1038/nature06171
Date:
23-Jul-07     Release date:   16-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52917  (VPS4_YEAST) -  Vacuolar protein sorting-associated protein 4
Seq:
Struc:
437 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P36108  (DID4_YEAST) -  DOA4-independent degradation protein 4
Seq:
Struc:
232 a.a.
41 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1038/nature06171 Nature 449:735-739 (2007)
PubMed id: 17928861  
 
 
Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4.
T.Obita, S.Saksena, S.Ghazi-Tabatabai, D.J.Gill, O.Perisic, S.D.Emr, R.L.Williams.
 
  ABSTRACT  
 
The AAA+ ATPases are essential for various activities such as membrane trafficking, organelle biogenesis, DNA replication, intracellular locomotion, cytoskeletal remodelling, protein folding and proteolysis. The AAA ATPase Vps4, which is central to endosomal traffic to lysosomes, retroviral budding and cytokinesis, dissociates ESCRT complexes (the endosomal sorting complexes required for transport) from membranes. Here we show that, of the six ESCRT--related subunits in yeast, only Vps2 and Did2 bind the MIT (microtubule interacting and transport) domain of Vps4, and that the carboxy-terminal 30 residues of the subunits are both necessary and sufficient for interaction. We determined the crystal structure of the Vps2 C terminus in a complex with the Vps4 MIT domain, explaining the basis for selective ESCRT-III recognition. MIT helices alpha2 and alpha3 recognize a (D/E)xxLxxRLxxL(K/R) motif, and mutations within this motif cause sorting defects in yeast. Our crystal structure of the amino-terminal domain of an archaeal AAA ATPase of unknown function shows that it is closely related to the MIT domain of Vps4. The archaeal ATPase interacts with an archaeal ESCRT-III-like protein even though these organisms have no endomembrane system, suggesting that the Vps4/ESCRT-III partnership is a relic of a function that pre-dates the divergence of eukaryotes and Archaea.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Characterization of the Vps4–Vps2 complex. a, GST-tagged MIT domain of yeast Vps4 and full-length Vps4 interact with full-length Vps2. Coomassie-stained SDS–PAGE shows the material bound to the glutathione-Sepharose resin. b, c, Vps2 C-terminal constructs (residues 106–232 in b and residues 120–232 in c) also interact with an untagged MIT domain as detected by band-shift on native PAGE. d, Vps2 C-terminal region (residues 183–232) binds to the FlAsH-tagged Vps4 MIT domain with a K[d] of 28 M. e, Structure of the complex between Vps2 (cyan) and the Vps4 MIT domain (yellow). f, Interactions between Vps2 C and MIT domain. g, The distinctive three-corners-of-a-square appearance of the three-helix MIT bundle. h–j, Enlarged central (i) and peripheral Vps2 helix C specificity determinants (N-terminal and C-terminal regions are shown in h and j, respectively).
Figure 3.
Figure 3: MIT-interacting motifs in Vps2 and Did2 are important for function in vivo. a, In wild-type cells, GFP-tagged carboxypeptidase-S accumulates in the vacuolar lumen (FM4-64 preferentially labels the limiting membrane of the vacuole). A single mutation at position 0 of the Vps2 MIM (R224D) impairs sorting, and the GFP–CPS accumulates in the limiting membrane of the vacuole. A double mutation of the Vps2 MIM (L228D/K229D) causes GFP–CPS accumulation in a class E compartment. b, Both a single mutation at position 0 of the Did2 MIM (R198D) and a double mutation (L199D/L202D) impair sorting of GFP–CPS, which accumulates in the limiting membrane of the vacuole.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 735-739) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220121 B.Różycki, Y.C.Kim, and G.Hummer (2011).
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions.
  Structure, 19, 109-116.  
21332354 J.H.Hurley, and H.Stenmark (2011).
Molecular mechanisms of ubiquitin-dependent membrane traffic.
  Annu Rev Biophys, 40, 119-142.  
21677686 J.Martin-Serrano, and S.J.Neil (2011).
Host factors involved in retroviral budding and release.
  Nat Rev Microbiol, 9, 519-531.  
21263029 M.Wemmer, I.Azmi, M.West, B.Davies, D.Katzmann, and G.Odorizzi (2011).
Bro1 binding to Snf7 regulates ESCRT-III membrane scission activity in yeast.
  J Cell Biol, 192, 295-306.  
21030261 S.Peel, P.Macheboeuf, N.Martinelli, and W.Weissenhorn (2011).
Divergent pathways lead to ESCRT-III-catalyzed membrane fission.
  Trends Biochem Sci, 36, 199-210.  
20362686 A.Hervás-Aguilar, O.Rodríguez-Galán, A.Galindo, J.F.Abenza, H.N.Arst, and M.A.Peñalva (2010).
Characterization of Aspergillus nidulans DidB Did2, a non-essential component of the multivesicular body pathway.
  Fungal Genet Biol, 47, 636-646.  
19963362 A.Roll-Mecak, and F.J.McNally (2010).
Microtubule-severing enzymes.
  Curr Opin Cell Biol, 22, 96.  
20110351 A.Shestakova, A.Hanono, S.Drosner, M.Curtiss, B.A.Davies, D.J.Katzmann, and M.Babst (2010).
Assembly of the AAA ATPase Vps4 on ESCRT-III.
  Mol Biol Cell, 21, 1059-1071.  
20702581 B.A.Davies, I.F.Azmi, J.Payne, A.Shestakova, B.F.Horazdovsky, M.Babst, and D.J.Katzmann (2010).
Coordination of substrate binding and ATP hydrolysis in Vps4-mediated ESCRT-III disassembly.
  Mol Biol Cell, 21, 3396-3408.  
20719964 B.Renvoisé, R.L.Parker, D.Yang, J.C.Bakowska, J.H.Hurley, and C.Blackstone (2010).
SPG20 protein spartin is recruited to midbodies by ESCRT-III protein Ist1 and participates in cytokinesis.
  Mol Biol Cell, 21, 3293-3303.  
20089837 D.P.Nickerson, M.West, R.Henry, and G.Odorizzi (2010).
Regulators of Vps4 ATPase activity at endosomes differentially influence the size and rate of formation of intralumenal vesicles.
  Mol Biol Cell, 21, 1023-1032.  
20134403 D.Teis, S.Saksena, B.L.Judson, and S.D.Emr (2010).
ESCRT-II coordinates the assembly of ESCRT-III filaments for cargo sorting and multivesicular body vesicle formation.
  EMBO J, 29, 871-883.  
20223751 H.Urwin, A.Authier, J.E.Nielsen, D.Metcalf, C.Powell, K.Froud, D.S.Malcolm, I.Holm, P.Johannsen, J.Brown, E.M.Fisher, J.van der Zee, M.Bruyland, C.Van Broeckhoven, J.Collinge, S.Brandner, C.Futter, and A.M.Isaacs (2010).
Disruption of endocytic trafficking in frontotemporal dementia with CHMP2B mutations.
  Hum Mol Genet, 19, 2228-2238.  
20588296 J.H.Hurley, and P.I.Hanson (2010).
Membrane budding and scission by the ESCRT machinery: it's all in the neck.
  Nat Rev Mol Cell Biol, 11, 556-566.  
  20653365 J.H.Hurley (2010).
The ESCRT complexes.
  Crit Rev Biochem Mol Biol, 45, 463-487.  
19828764 L.Corless, C.M.Crump, S.D.Griffin, and M.Harris (2010).
Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles.
  J Gen Virol, 91, 362-372.  
21050804 R.Bernander, and T.J.Ettema (2010).
FtsZ-less cell division in archaea and bacteria.
  Curr Opin Microbiol, 13, 747-752.  
20849418 Y.Osako, Y.Maemoto, R.Tanaka, H.Suzuki, H.Shibata, and M.Maki (2010).
Autolytic activity of human calpain 7 is enhanced by ESCRT-III-related protein IST1 through MIT-MIM interaction.
  FEBS J, 277, 4412-4426.  
18972064 A.F.Ellen, S.V.Albers, W.Huibers, A.Pitcher, C.F.Hobel, H.Schwarz, M.Folea, S.Schouten, E.J.Boekema, B.Poolman, and A.J.Driessen (2009).
Proteomic analysis of secreted membrane vesicles of archaeal Sulfolobus species reveals the presence of endosome sorting complex components.
  Extremophiles, 13, 67-79.  
19535732 B.McDonald, and J.Martin-Serrano (2009).
No strings attached: the ESCRT machinery in viral budding and cytokinesis.
  J Cell Sci, 122, 2167-2177.  
19325624 C.Raiborg, and H.Stenmark (2009).
The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins.
  Nature, 458, 445-452.  
19936052 G.Fabrikant, S.Lata, J.D.Riches, J.A.Briggs, W.Weissenhorn, and M.M.Kozlov (2009).
Computational model of membrane fission catalyzed by ESCRT-III.
  PLoS Comput Biol, 5, e1000575.  
18835459 J.B.Dacks, A.A.Peden, and M.C.Field (2009).
Evolution of specificity in the eukaryotic endomembrane system.
  Int J Biochem Cell Biol, 41, 330-340.  
19307607 J.H.Boysen, S.Fanning, J.Newberg, R.F.Murphy, and A.P.Mitchell (2009).
Detection of protein-protein interactions through vesicle targeting.
  Genetics, 182, 33-39.  
19477918 J.Xiao, X.W.Chen, B.A.Davies, A.R.Saltiel, D.J.Katzmann, and Z.Xu (2009).
Structural basis of Ist1 function and Ist1-Did2 interaction in the multivesicular body pathway and cytokinesis.
  Mol Biol Cell, 20, 3514-3524.
PDB codes: 3ggy 3ggz
19129480 M.Agromayor, J.G.Carlton, J.P.Phelan, D.R.Matthews, L.M.Carlin, S.Ameer-Beg, K.Bowers, and J.Martin-Serrano (2009).
Essential role of hIST1 in cytokinesis.
  Mol Biol Cell, 20, 1374-1387.  
19129479 M.Bajorek, E.Morita, J.J.Skalicky, S.G.Morham, M.Babst, and W.I.Sundquist (2009).
Biochemical analyses of human IST1 and its function in cytokinesis.
  Mol Biol Cell, 20, 1360-1373.  
19525971 M.Bajorek, H.L.Schubert, J.McCullough, C.Langelier, D.M.Eckert, W.M.Stubblefield, N.T.Uter, D.G.Myszka, C.P.Hill, and W.I.Sundquist (2009).
Structural basis for ESCRT-III protein autoinhibition.
  Nat Struct Mol Biol, 16, 754-762.
PDB codes: 3frr 3frs 3frt 3frv
19201590 M.C.Field, and J.B.Dacks (2009).
First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes.
  Curr Opin Cell Biol, 21, 4.  
19056728 O.Rodríguez-Galán, A.Galindo, A.Hervás-Aguilar, H.N.Arst, and M.A.Peñalva (2009).
Physiological Involvement in pH Signaling of Vps24-mediated Recruitment of Aspergillus PalB Cysteine Protease to ESCRT-III.
  J Biol Chem, 284, 4404-4412.  
19560911 P.I.Hanson, S.Shim, and S.A.Merrill (2009).
Cell biology of the ESCRT machinery.
  Curr Opin Cell Biol, 21, 568-574.  
19725809 P.Weiss, S.Huppert, and R.Kölling (2009).
Analysis of the dual function of the ESCRT-III protein Snf7 in endocytic trafficking and in gene expression.
  Biochem J, 424, 89-97.  
19783442 R.Y.Samson, and S.D.Bell (2009).
Ancient ESCRTs and the evolution of binary fission.
  Trends Microbiol, 17, 507-513.  
19135892 S.Saksena, J.Wahlman, D.Teis, A.E.Johnson, and S.D.Emr (2009).
Functional reconstitution of ESCRT-III assembly and disassembly.
  Cell, 136, 97.  
19307600 S.W.Eastman, M.Yassaee, and P.D.Bieniasz (2009).
A role for ubiquitin ligases and Spartin/SPG20 in lipid droplet turnover.
  J Cell Biol, 184, 881-894.  
19580544 T.L.Edwards, V.E.Clowes, H.T.Tsang, J.W.Connell, C.M.Sanderson, J.P.Luzio, and E.Reid (2009).
Endogenous spartin (SPG20) is recruited to endosomes and lipid droplets and interacts with the ubiquitin E3 ligases AIP4 and AIP5.
  Biochem J, 423, 31-39.  
19234443 T.Wollert, C.Wunder, J.Lippincott-Schwartz, and J.H.Hurley (2009).
Membrane scission by the ESCRT-III complex.
  Nature, 458, 172-177.  
19535731 T.Wollert, D.Yang, X.Ren, H.H.Lee, Y.J.Im, and J.H.Hurley (2009).
The ESCRT machinery at a glance.
  J Cell Sci, 122, 2163-2166.  
19686684 Y.J.Im, T.Wollert, E.Boura, and J.H.Hurley (2009).
Structure and function of the ESCRT-II-III interface in multivesicular body biogenesis.
  Dev Cell, 17, 234-243.
PDB code: 3htu
18987308 A.C.Lindås, E.A.Karlsson, M.T.Lindgren, T.J.Ettema, and R.Bernander (2008).
A unique cell division machinery in the Archaea.
  Proc Natl Acad Sci U S A, 105, 18942-18946.  
18606141 C.Kieffer, J.J.Skalicky, E.Morita, I.De Domenico, D.M.Ward, J.Kaplan, and W.I.Sundquist (2008).
Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding.
  Dev Cell, 15, 62-73.
PDB code: 2k3w
18316332 C.Yorikawa, E.Takaya, Y.Osako, R.Tanaka, Y.Terasawa, T.Hamakubo, Y.Mochizuki, H.Iwanari, T.Kodama, T.Maeda, K.Hitomi, H.Shibata, and M.Maki (2008).
Human calpain 7/PalBH associates with a subset of ESCRT-III-related proteins in its N-terminal region and partly localizes to endocytic membrane compartments.
  J Biochem, 143, 731-745.  
18997780 D.Yang, N.Rismanchi, B.Renvoisé, J.Lippincott-Schwartz, C.Blackstone, and J.H.Hurley (2008).
Structural basis for midbody targeting of spastin by the ESCRT-III protein CHMP1B.
  Nat Struct Mol Biol, 15, 1278-1286.
PDB code: 3eab
18222686 J.H.Hurley (2008).
ESCRT complexes and the biogenesis of multivesicular bodies.
  Curr Opin Cell Biol, 20, 4.  
18511562 J.McCullough, R.D.Fisher, F.G.Whitby, W.I.Sundquist, and C.P.Hill (2008).
ALIX-CHMP4 interactions in the human ESCRT pathway.
  Proc Natl Acad Sci U S A, 105, 7687-7691.
PDB codes: 3c3o 3c3q 3c3r
18194651 J.Xiao, H.Xia, J.Zhou, I.F.Azmi, B.A.Davies, D.J.Katzmann, and Z.Xu (2008).
Structural basis of Vta1 function in the multivesicular body sorting pathway.
  Dev Cell, 14, 37-49.
PDB codes: 2rkk 2rkl
18637903 K.F.Leung, J.B.Dacks, and M.C.Field (2008).
Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage.
  Traffic, 9, 1698-1716.  
18250627 K.U.Wendt, M.S.Weiss, P.Cramer, and D.W.Heinz (2008).
Structures and diseases.
  Nat Struct Mol Biol, 15, 117-120.  
18429951 N.Tanaka, M.Kyuuma, and K.Sugamura (2008).
Endosomal sorting complex required for transport proteins in cancer pathogenesis, vesicular transport, and non-endosomal functions.
  Cancer Sci, 99, 1293-1303.  
18209100 P.I.Hanson, R.Roth, Y.Lin, and J.E.Heuser (2008).
Plasma membrane deformation by circular arrays of ESCRT-III protein filaments.
  J Cell Biol, 180, 389-402.  
18266866 P.R.Vajjhala, C.H.Nguyen, M.J.Landsberg, C.Kistler, A.L.Gan, G.F.King, B.Hankamer, and A.L.Munn (2008).
The Vps4 C-terminal helix is a critical determinant for assembly and ATPase activity and has elements conserved in other members of the meiotic clade of AAA ATPases.
  FEBS J, 275, 1427-1449.  
19008417 R.Y.Samson, T.Obita, S.M.Freund, R.L.Williams, and S.D.Bell (2008).
A role for the ESCRT system in cell division in archaea.
  Science, 322, 1710-1713.
PDB code: 2w2u
18786397 S.Ghazi-Tabatabai, S.Saksena, J.M.Short, A.V.Pobbati, D.B.Veprintsev, R.A.Crowther, S.D.Emr, E.H.Egelman, and R.L.Williams (2008).
Structure and disassembly of filaments formed by the ESCRT-III subunit Vps24.
  Structure, 16, 1345-1356.  
18687924 S.Lata, G.Schoehn, A.Jain, R.Pires, J.Piehler, H.G.Gottlinger, and W.Weissenhorn (2008).
Helical structures of ESCRT-III are disassembled by VPS4.
  Science, 321, 1354-1357.  
18032584 S.M.Rue, S.Mattei, S.Saksena, and S.D.Emr (2008).
Novel ist1-did2 complex functions at a late step in multivesicular body sorting.
  Mol Biol Cell, 19, 475-484.  
18385515 S.Shim, S.A.Merrill, and P.I.Hanson (2008).
Novel interactions of ESCRT-III with LIP5 and VPS4 and their implications for ESCRT-III disassembly.
  Mol Biol Cell, 19, 2661-2672.  
18280501 Z.Yu, M.D.Gonciarz, W.I.Sundquist, C.P.Hill, and G.J.Jensen (2008).
Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p.
  J Mol Biol, 377, 364-377.  
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 codes are shown on the right.