PDBsum entry 2k3w

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protein Protein-protein interface(s) links
Protein transport PDB id
Protein chains
73 a.a. *
12 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Nmr structure of vps4a-mit-chmp6
Structure: Vacuolar protein sorting-associating protein 4a. Chain: a. Fragment: mit domain. Synonym: protein skd2, hvps4, vps4-1. Engineered: yes. Charged multivesicular body protein 6. Chain: b. Fragment: residues 166-181. Synonym: chromatin-modifying protein 6, vacuolar protein
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: vps4a, vps4. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: chmp6, vps20.
NMR struc: 20 models
Authors: C.Kieffer,J.J.Skalicky,E.Morita,I.De Domini,D.M.Ward, J.Kaplan,W.I.Sundquist
Key ref:
C.Kieffer et al. (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. PubMed id: 18606141 DOI: 10.1016/j.devcel.2008.05.014
19-May-08     Release date:   28-Oct-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9UN37  (VPS4A_HUMAN) -  Vacuolar protein sorting-associated protein 4A
437 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
Q96FZ7  (CHMP6_HUMAN) -  Charged multivesicular body protein 6
201 a.a.
12 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


DOI no: 10.1016/j.devcel.2008.05.014 Dev Cell 15:62-73 (2008)
PubMed id: 18606141  
Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding.
C.Kieffer, J.J.Skalicky, E.Morita, I.De Domenico, D.M.Ward, J.Kaplan, W.I.Sundquist.
The ESCRT pathway mediates membrane remodeling during enveloped virus budding, cytokinesis, and intralumenal endosomal vesicle formation. Late in the pathway, a subset of membrane-associated ESCRT-III proteins display terminal amphipathic "MIM1" helices that bind and recruit VPS4 ATPases via their MIT domains. We now report that VPS4 MIT domains also bind a second, "MIM2" motif found in a different subset of ESCRT-III subunits. The solution structure of the VPS4 MIT-CHMP6 MIM2 complex revealed that MIM2 elements bind in extended conformations along the groove between the first and third helices of the MIT domain. Mutations that block VPS4 MIT-MIM2 interactions inhibit VPS4 recruitment, lysosomal protein targeting, and HIV-1 budding. MIT-MIM2 interactions appear to be common throughout the ESCRT pathway and possibly elsewhere, and we suggest how these interactions could contribute to a mechanism in which VPS4 and ESCRT-III proteins function together to constrict the necks of budding vesicles.
  Selected figure(s)  
Figure 3.
Figure 3. Mutational Analyses of the VPS4A MIT-CHMP6 Complex
(A) Biosensor binding isotherms showing VPS4A MIT binding to wild-type and mutant CHMP6 MIM2 peptides (labeled). Note that the CHMP6 L178D mutation reduces the binding affinity vert, similar 8-fold (from K[D] = 5.8 ± 0.8 to K[D] = 44.4 ± 0.2 μM), whereas the L170D and V173D mutations block all detectable binding.
(B) Biosensor binding isotherms showing that the V13D mutation in VPS4A MIT helix 1 blocks CHMP6 MIM2 binding (triangles) but does not affect CHMP1B MIM1 binding (ovals).
(C) Biosensor binding isotherms showing that the L64D mutation in VPS4A MIT helix 3 blocks CHMP1B MIM1 binding (ovals), but had a much more modest effect on CHMP6 MIM2 binding (triangles), altering CHMP6 MIM2 binding from K[D] = 5.8 ± 0.8 μM to K[D] = 26.1 ± 0.8 μM.
Figure 7.
Figure 7. Model for VPS4 Recruitment and ESCRT-III Filament Constriction
Schematic model showing how different ESCRT-III subunits (blue and green) could coassemble into concentric rings that display C-terminal MIM1 (green) and internal MIM2 (blue) elements, thereby creating a high-affinity VPS4 binding surface (orange, with the three helices of the MIT domains in red, orange, and yellow). Recruited VPS4 ATPases could then remove individual ESCRT-III subunits, constricting the rings about cargoes (red) and thereby helping to drive vesicle extrusion and neck closure (see text for full details). We note that six molecules of the Vps4 activator, Vta1p/LIP5, also bind the VPS4 beta domains and make additional MIT-ESCRT-III interactions, but for clarity these additional interactions are not shown.
  The above figures are reprinted from an Open Access publication published by Cell Press: Dev Cell (2008, 15, 62-73) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21396898 E.Morita, V.Sandrin, J.McCullough, A.Katsuyama, I.Baci Hamilton, and W.I.Sundquist (2011).
ESCRT-III protein requirements for HIV-1 budding.
  Cell Host Microbe, 9, 235-242.  
21332354 J.H.Hurley, and H.Stenmark (2011).
Molecular mechanisms of ubiquitin-dependent membrane traffic.
  Annu Rev Biophys, 40, 119-142.  
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.  
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.  
20427536 E.Popova, S.Popov, and H.G.Göttlinger (2010).
Human immunodeficiency virus type 1 nucleocapsid p1 confers ESCRT pathway dependence.
  J Virol, 84, 6590-6597.  
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.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
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.  
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.  
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
19560911 P.I.Hanson, S.Shim, and S.A.Merrill (2009).
Cell biology of the ESCRT machinery.
  Curr Opin Cell Biol, 21, 568-574.  
19783442 R.Y.Samson, and S.D.Bell (2009).
Ancient ESCRTs and the evolution of binary fission.
  Trends Microbiol, 17, 507-513.  
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.  
19282983 V.Dussupt, M.P.Javid, G.Abou-Jaoudé, J.A.Jadwin, La Cruz, K.Nagashima, and F.Bouamr (2009).
The nucleocapsid region of HIV-1 Gag cooperates with the PTAP and LYPXnL late domains to recruit the cellular machinery necessary for viral budding.
  PLoS Pathog, 5, e1000339.  
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
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
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
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.