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PDBsum entry 2dfs

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protein Protein-protein interface(s) links
Contractile protein/transport protein PDB id
2dfs
Jmol
Contents
Protein chains
994 a.a. *
(+ 6 more) 139 a.a. *
* Residue conservation analysis
PDB id:
2dfs
Name: Contractile protein/transport protein
Title: 3-d structure of myosin-v inhibited state
Structure: Myosin-5a. Chain: a, m. Fragment: residues 1-1080. Synonym: myosin va, dilute myosin heavy chain, non-muscle, heavy chain p190, myosin-v. Engineered: yes. Calmodulin. Chain: b, c, d, e, f, g, n, o, p, q, r, s. Synonym: cam.
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Mus musculus. House mouse. Organism_taxid: 10090.
Authors: J.Liu,D.W.Taylor,E.B.Krementsova,K.M.Trybus,K.A.Taylor
Key ref:
J.Liu et al. (2006). Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography. Nature, 442, 208-211. PubMed id: 16625208 DOI: 10.1038/nature04719
Date:
03-Mar-06     Release date:   25-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q02440  (MYO5A_CHICK) -  Unconventional myosin-Va
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1829 a.a.
994 a.a.
Protein chains
Pfam   ArchSchema ?
P62204  (CALM_MOUSE) -  Calmodulin
Seq:
Struc:
149 a.a.
139 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   11 terms 
  Biological process     regulation of cytokinesis   12 terms 
  Biochemical function     protein phosphatase activator activity     10 terms  

 

 
DOI no: 10.1038/nature04719 Nature 442:208-211 (2006)
PubMed id: 16625208  
 
 
Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography.
J.Liu, D.W.Taylor, E.B.Krementsova, K.M.Trybus, K.A.Taylor.
 
  ABSTRACT  
 
Unconventional myosin V (myoV) is an actin-based molecular motor that has a key function in organelle and mRNA transport, as well as in membrane trafficking. MyoV was the first member of the myosin superfamily shown to be processive, meaning that a single motor protein can 'walk' hand-over-hand along an actin filament for many steps before detaching. Full-length myoV has a low actin-activated MgATPase activity at low [Ca2+], whereas expressed constructs lacking the cargo-binding domain have a high activity regardless of [Ca2+] (refs 5-7). Hydrodynamic data and electron micrographs indicate that the active state is extended, whereas the inactive state is compact. Here we show the first three-dimensional structure of the myoV inactive state. Each myoV molecule consists of two heads that contain an amino-terminal motor domain followed by a lever arm that binds six calmodulins. The heads are followed by a coiled-coil dimerization domain (S2) and a carboxy-terminal globular cargo-binding domain. In the inactive structure, bending of myoV at the head-S2 junction places the cargo-binding domain near the motor domain's ATP-binding pocket, indicating that ATPase inhibition might occur through decreased rates of nucleotide exchange. The actin-binding interfaces are unobstructed, and the lever arm is oriented in a position typical of strong actin-binding states. This structure indicates that motor recycling after cargo delivery might occur through transport on actively treadmilling actin filaments rather than by diffusion.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Molecular arrangement within the 'flower' motif. a, At the top is an opaque surface rendering viewed from the solvent phase; at the bottom is a translucent surface view with the myoV atomic model rendered in space filling. The colour scheme for the bottom molecule is as follows: red and magenta, motor domains; green, light chains; blue, heavy chain component of the lever arm; cyan, S2 domain; yellow, cargo-binding domain density envelope; grey, adjacent molecules. b, c, Higher-magnification views showing the motor domain fit into the density envelope. b, View from the solvent phase; c, view from the monolayer side.
Figure 4.
Figure 4: Orientation of the myoV-inhibited structure on F-actin. F-actin strands rendered light blue and grey. Actin docking is based on ref. 30. a, Panel shows F-actin can bind only one myoV head at a time. The unbound head extends up towards the viewer. b, Same view direction as a but with the second head docked. c, High-magnification gallery of actin-bound myoV molecules. In some the S2 domain can be seen between the two heads. Drying in negative stain would flatten the structure onto a plane, which may account for some of the differences between the models and the micrographs.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 442, 208-211) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935055 C.L.Lawson, M.L.Baker, C.Best, C.Bi, M.Dougherty, P.Feng, G.van Ginkel, B.Devkota, I.Lagerstedt, S.J.Ludtke, R.H.Newman, T.J.Oldfield, I.Rees, G.Sahni, R.Sala, S.Velankar, J.Warren, J.D.Westbrook, K.Henrick, G.J.Kleywegt, H.M.Berman, and W.Chiu (2011).
EMDataBank.org: unified data resource for CryoEM.
  Nucleic Acids Res, 39, D456-D464.  
21326200 C.Veigel, and C.F.Schmidt (2011).
Moving into the cell: single-molecule studies of molecular motors in complex environments.
  Nat Rev Mol Cell Biol, 12, 163-176.  
20938697 J.Tilsner, K.Amari, and L.Torrance (2011).
Plasmodesmata viewed as specialised membrane adhesion sites.
  Protoplasma, 248, 39-60.  
20439999 A.Heuck, I.Fetka, D.N.Brewer, D.Hüls, M.Munson, R.P.Jansen, and D.Niessing (2010).
The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.
  J Cell Biol, 189, 497-510.
PDB code: 3mmi
21081082 C.F.Song, K.Sader, H.White, J.Kendrick-Jones, and J.Trinick (2010).
Nucleotide-dependent shape changes in the reverse direction motor, myosin VI.
  Biophys J, 99, 3336-3344.  
20888479 J.Liu, E.R.Wright, and H.Winkler (2010).
3D visualization of HIV virions by cryoelectron tomography.
  Methods Enzymol, 483, 267-290.  
20149155 T.Kögel, R.Rudolf, E.Hodneland, A.Hellwig, S.A.Kuznetsov, F.Seiler, T.H.Söllner, J.Barroso, and H.H.Gerdes (2010).
Distinct roles of myosin Va in membrane remodeling and exocytosis of secretory granules.
  Traffic, 11, 637-650.  
20006949 A.Nagy, G.Piszczek, and J.R.Sellers (2009).
Extensibility of the extended tail domain of processive and nonprocessive myosin V molecules.
  Biophys J, 97, 3123-3131.  
19397789 C.O.Sanchez Sorzano, C.Messaoudi, M.Eibauer, J.Bilbao-Castro, R.Hegerl, S.Nickell, S.Marco, and J.Carazo (2009).
Marker-free image registration of electron tomography tilt-series.
  BMC Bioinformatics, 10, 124.  
19822760 E.M.Craig, and H.Linke (2009).
Mechanochemical model for myosin V.
  Proc Natl Acad Sci U S A, 106, 18261-18266.  
19032983 H.Winkler, P.Zhu, J.Liu, F.Ye, K.H.Roux, and K.A.Taylor (2009).
Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes.
  J Struct Biol, 165, 64-77.  
19429612 J.Liu, T.Lin, D.J.Botkin, E.McCrum, H.Winkler, and S.J.Norris (2009).
Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: evidence for stator ring curvature and rotor/C-ring assembly flexion.
  J Bacteriol, 191, 5026-5036.  
19398338 M.L.Kerber, D.T.Jacobs, L.Campagnola, B.D.Dunn, T.Yin, A.D.Sousa, O.A.Quintero, and R.E.Cheney (2009).
A novel form of motility in filopodia revealed by imaging myosin-X at the single-molecule level.
  Curr Biol, 19, 967-973.  
19148887 P.Yuan, X.Zhou, H.Wang, N.Liu, Y.Hu, G.J.Auchterlonie, J.Drennan, X.Yao, G.Q.Lu, J.Zou, and C.Yu (2009).
Electron-tomography determination of the packing structure of macroporous ordered siliceous foams assembled from vesicles.
  Small, 5, 377-382.  
19452133 W.Hwang, and M.J.Lang (2009).
Mechanical design of translocating motor proteins.
  Cell Biochem Biophys, 54, 11-22.  
18585038 A.K.Satoh, B.X.Li, H.Xia, and D.F.Ready (2008).
Calcium-activated Myosin V closes the Drosophila pupil.
  Curr Biol, 18, 951-955.  
18221262 E.C.Casavola, A.Catucci, P.Bielli, A.Di Pentima, G.Porcu, M.Pennestri, D.O.Cicero, and A.Ragnini-Wilson (2008).
Ypt32p and Mlc1p bind within the vesicle binding region of the class V myosin Myo2p globular tail domain.
  Mol Microbiol, 67, 1051-1066.  
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.  
18405917 F.Ye, J.Liu, H.Winkler, and K.A.Taylor (2008).
Integrin alpha IIb beta 3 in a membrane environment remains the same height after Mn2+ activation when observed by cryoelectron tomography.
  J Mol Biol, 378, 976-986.  
17945510 G.B.Hu, W.J.Rice, S.Dröse, K.Altendorf, and D.L.Stokes (2008).
Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals.
  J Struct Biol, 161, 411-418.  
18503043 I.A.Sparkes, N.A.Teanby, and C.Hawes (2008).
Truncated myosin XI tail fusions inhibit peroxisome, Golgi, and mitochondrial movement in tobacco leaf epidermal cells: a genetic tool for the next generation.
  J Exp Bot, 59, 2499-2512.  
18226515 J.L.Ross, M.Y.Ali, and D.M.Warshaw (2008).
Cargo transport: molecular motors navigate a complex cytoskeleton.
  Curr Opin Cell Biol, 20, 41-47.  
18266909 J.W.Hammond, K.Griffin, G.T.Jih, J.Stuckey, and K.J.Verhey (2008).
Co-operative versus independent transport of different cargoes by Kinesin-1.
  Traffic, 9, 725-741.  
18239852 K.M.Trybus (2008).
Myosin V from head to tail.
  Cell Mol Life Sci, 65, 1378-1389.  
18330901 M.C.Pranchevicius, M.M.Baqui, H.C.Ishikawa-Ankerhold, E.V.Lourenço, R.M.Leão, S.R.Banzi, C.T.dos Santos, M.C.Barreira, E.M.Espreafico, and R.E.Larson (2008).
Myosin Va phosphorylated on Ser1650 is found in nuclear speckles and redistributes to nucleoli upon inhibition of transcription.
  Cell Motil Cytoskeleton, 65, 441-456.  
18441369 N.M.Kad, K.M.Trybus, and D.M.Warshaw (2008).
Load and Pi control flux through the branched kinetic cycle of myosin V.
  J Biol Chem, 283, 17477-17484.  
18044718 R.D.Eppinga, I.F.Peng, J.L.Lin, C.F.Wu, and J.J.Lin (2008).
Opposite effects of overexpressed myosin Va or heavy meromyosin Va on vesicle distribution, cytoskeleton organization, and cell motility in nonmuscle cells.
  Cell Motil Cytoskeleton, 65, 197-215.  
18216256 X.D.Li, H.S.Jung, Q.Wang, R.Ikebe, R.Craig, and M.Ikebe (2008).
The globular tail domain puts on the brake to stop the ATPase cycle of myosin Va.
  Proc Natl Acad Sci U S A, 105, 1140-1145.  
18755273 Y.Fujiyoshi, and N.Unwin (2008).
Electron crystallography of proteins in membranes.
  Curr Opin Struct Biol, 18, 587-592.  
18984164 Z.Wang, J.G.Edwards, N.Riley, D.W.Provance, R.Karcher, X.D.Li, I.G.Davison, M.Ikebe, J.A.Mercer, J.A.Kauer, and M.D.Ehlers (2008).
Myosin Vb mobilizes recycling endosomes and AMPA receptors for postsynaptic plasticity.
  Cell, 135, 535-548.  
18056806 A.Heuck, T.G.Du, S.Jellbauer, K.Richter, C.Kruse, S.Jaklin, M.Müller, J.Buchner, R.P.Jansen, and D.Niessing (2007).
Monomeric myosin V uses two binding regions for the assembly of stable translocation complexes.
  Proc Natl Acad Sci U S A, 104, 19778-19783.  
17200416 D.Cai, A.D.Hoppe, J.A.Swanson, and K.J.Verhey (2007).
Kinesin-1 structural organization and conformational changes revealed by FRET stoichiometry in live cells.
  J Cell Biol, 176, 51-63.  
17561414 D.W.Taylor, D.F.Kelly, A.Cheng, and K.A.Taylor (2007).
On the freezing and identification of lipid monolayer 2-D arrays for cryoelectron microscopy.
  J Struct Biol, 160, 305-312.  
17175153 H.L.Sweeney, and A.Houdusse (2007).
What can myosin VI do in cells?
  Curr Opin Cell Biol, 19, 57-66.  
17374717 J.A.Hammer, and X.Wu (2007).
Slip sliding away with myosin V.
  Proc Natl Acad Sci U S A, 104, 5255-5256.  
17628590 J.Bosch, S.Turley, C.M.Roach, T.M.Daly, L.W.Bergman, and W.G.Hol (2007).
The closed MTIP-myosin A-tail complex from the malaria parasite invasion machinery.
  J Mol Biol, 372, 77-88.
PDB code: 2qac
17638580 J.E.Norville, D.F.Kelly, T.F.Knight, A.M.Belcher, and T.Walz (2007).
7A projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals.
  J Struct Biol, 160, 313-323.  
18427938 J.R.Sellers, and P.J.Knight (2007).
Folding and regulation in myosins II and V.
  J Muscle Res Cell Motil, 28, 363-370.  
17403927 J.S.Au, C.Puri, G.Ihrke, J.Kendrick-Jones, and F.Buss (2007).
Myosin VI is required for sorting of AP-1B-dependent cargo to the basolateral domain in polarized MDCK cells.
  J Cell Biol, 177, 103-114.  
17208425 K.A.Taylor (2007).
Regulation and recycling of myosin V.
  Curr Opin Cell Biol, 19, 67-74.  
17562702 K.M.Trybus, M.I.Gushchin, H.Lui, L.Hazelwood, E.B.Krementsova, N.Volkmann, and D.Hanein (2007).
Effect of calcium on calmodulin bound to the IQ motifs of myosin V.
  J Biol Chem, 282, 23316-23325.  
17360524 M.Y.Ali, E.B.Krementsova, G.G.Kennedy, R.Mahaffy, T.D.Pollard, K.M.Trybus, and D.M.Warshaw (2007).
Myosin Va maneuvers through actin intersections and diffuses along microtubules.
  Proc Natl Acad Sci U S A, 104, 4332-4336.  
17363376 O.Sato, X.D.Li, and M.Ikebe (2007).
Myosin Va becomes a low duty ratio motor in the inhibited form.
  J Biol Chem, 282, 13228-13239.  
17189480 Q.Wang, M.A.Deloia, Y.Kang, C.Litchke, N.Zhang, M.A.Titus, and K.J.Walters (2007).
The SH3 domain of a M7 interacts with its C-terminal proline-rich region.
  Protein Sci, 16, 189-196.
PDB code: 2i0n
17151196 A.Houdusse, J.F.Gaucher, E.Krementsova, S.Mui, K.M.Trybus, and C.Cohen (2006).
Crystal structure of apo-calmodulin bound to the first two IQ motifs of myosin V reveals essential recognition features.
  Proc Natl Acad Sci U S A, 103, 19326-19331.
PDB code: 2ix7
16921171 A.O.Olivares, W.Chang, M.S.Mooseker, D.D.Hackney, and E.M.De La Cruz (2006).
The tail domain of myosin Va modulates actin binding to one head.
  J Biol Chem, 281, 31326-31336.  
17012238 B.Salzameda, K.C.Facemyer, B.W.Beck, and C.R.Cremo (2006).
The N-terminal lobes of both regulatory light chains interact with the tail domain in the 10 S-inhibited conformation of smooth muscle myosin.
  J Biol Chem, 281, 38801-38811.  
16920704 H.Lu, E.B.Krementsova, and K.M.Trybus (2006).
Regulation of myosin V processivity by calcium at the single molecule level.
  J Biol Chem, 281, 31987-31994.  
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.