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- EMDB-1201: Three-dimensional structure of the myosin V inhibited state by cr... -

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Basic information

Entry
Database: EMDB / ID: EMD-1201
TitleThree-dimensional structure of the myosin V inhibited state by cryoelectron tomography.
Map dataThis the 3-D average map of myosin-V in "off" state
Sample
  • Sample: MYOSIN V
  • Protein or peptide: Myosin-V
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol ...CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / minus-end directed microfilament motor activity / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / insulin-responsive compartment / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / : / establishment of protein localization to mitochondrial membrane / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / vesicle transport along actin filament / myosin complex / regulation of synaptic vesicle endocytosis / microfilament motor activity / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / filamentous actin / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / vesicle-mediated transport / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / actin filament organization / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / protein localization to plasma membrane / mitochondrial membrane / positive regulation of receptor signaling pathway via JAK-STAT / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion / cellular response to insulin stimulus / calcium-dependent protein binding / disordered domain specific binding
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 / Unconventional myosin-Va
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 24.0 Å
AuthorsLiu J / Taylor DW / Krementsova EB / Trybus KM / Taylor KA
CitationJournal: Nature / Year: 2006
Title: Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography.
Authors: Jun Liu / Dianne W Taylor / Elena B Krementsova / Kathleen M Trybus / Kenneth 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 ...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.
History
DepositionMar 1, 2006-
Header (metadata) releaseMar 2, 2006-
Map releaseJul 13, 2006-
UpdateMar 27, 2013-
Current statusMar 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.727346413
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.727346413
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  • Surface view with fitted model
  • Atomic models: PDB-2dfs
  • Surface level: 0.727346413
  • Imaged by UCSF Chimera
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  • Close-up
  • Surface view with fitted model
  • Atomic models: PDB-2dfs
  • Surface level: 0.727346413
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2dfs
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1201.gif

Downloads & links

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Map

FileDownload / File: emd_1201.map.gz / Format: CCP4 / Size: 7.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis the 3-D average map of myosin-V in "off" state
Voxel sizeX=Y=Z: 5.56 Å
Density
Contour LevelBy EMDB: 0.65 / Movie #1: 0.7273464
Minimum - Maximum-0.411051 - 13.8574
Average (Standard dev.)0.0420816 (±0.651013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-30
Dimensions18018060
Spacing18018060
CellA: 1000.8 Å / B: 1000.8 Å / C: 333.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.565.565.56
M x/y/z18018060
origin x/y/z0.0000.0000.000
length x/y/z1000.8001000.800333.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-80-80-79
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-90-90-30
NC/NR/NS18018060
D min/max/mean-0.41113.8570.042

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Supplemental data

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Sample components

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Entire : MYOSIN V

EntireName: MYOSIN V
Components
  • Sample: MYOSIN V
  • Protein or peptide: Myosin-V

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Supramolecule #1000: MYOSIN V

SupramoleculeName: MYOSIN V / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa

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Macromolecule #1: Myosin-V

MacromoleculeName: Myosin-V / type: protein_or_peptide / ID: 1 / Name.synonym: MYOV / Details: expressed full lengh myosin-V / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa
Recombinant expressionOrganism: Sf9 cells

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferDetails: 20 mM Na2HPO4, 80-100 mM NaCl, 2 mM MgCl2, 1 mM ADP, 1 mM EGTA
StainingType: NEGATIVE
Details: MyoV 2-D arrays were recovered from the lipid monolayer
GridDetails: 200 mesh copper grids covered with a reticulated carbon film.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: in house plunger / Method: Blot for 3 seconds before plunging
Detailscrystals grown on a lipid-monolayer

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 12.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 24000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 70 °
TemperatureAverage: 103 K
DateFeb 1, 2004
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Digitization - Sampling interval: 24 µm / Number real images: 360 / Average electron dose: 30 e/Å2

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Image processing

Crystal parametersUnit cell - A: 653 Å / Unit cell - B: 653 Å / Unit cell - γ: 120 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 6
CTF correctionDetails: focus gradient correction
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: protomo

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Atomic model buiding 1

SoftwareName: Situs and NMFF
DetailsProtocol: Rigid body and Normal Mode Flexible. Start with Rigid body docking by using SITUS and refine with NMFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation
Output model

PDB-2dfs:
3-D structure of Myosin-V inhibited state

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