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Yorodumi- 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 | |||||||||
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Title | Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography. | |||||||||
Map data | This the 3-D average map of myosin-V in "off" state | |||||||||
Sample |
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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 / presynaptic endocytosis / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / negative regulation of calcium ion transmembrane transporter activity / Smooth Muscle Contraction / minus-end directed microfilament motor activity / Ca2+ pathway / FCERI mediated Ca+2 mobilization / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / insulin-responsive compartment / RAF/MAP kinase cascade / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / vesicle transport along actin filament / : / Stimuli-sensing channels / establishment of protein localization to mitochondrial membrane / Ion homeostasis / type 3 metabotropic glutamate receptor binding / myosin complex / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / microfilament motor activity / regulation of cardiac muscle cell action potential / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / filamentous actin / : / calyx of Held / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / vesicle-mediated transport / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / actin filament organization / protein localization to plasma membrane / spindle microtubule / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion / mitochondrial membrane / cellular response to insulin stimulus / cellular response to type II interferon / G2/M transition of mitotic cell cycle / spindle pole Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / negative staining / Resolution: 24.0 Å | |||||||||
Authors | Liu J / Taylor DW / Krementsova EB / Trybus KM / Taylor KA | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1201.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-1201-v30.xml emd-1201.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | 1201.gif | 58.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1201 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1201 | HTTPS FTP |
-Validation report
Summary document | emd_1201_validation.pdf.gz | 271.9 KB | Display | EMDB validaton report |
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Full document | emd_1201_full_validation.pdf.gz | 271.5 KB | Display | |
Data in XML | emd_1201_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1201 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1201 | HTTPS FTP |
-Related structure data
Related structure data | 2dfsMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1201.map.gz / Format: CCP4 / Size: 7.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This the 3-D average map of myosin-V in "off" state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MYOSIN V
Entire | Name: MYOSIN V |
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Components |
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-Supramolecule #1000: MYOSIN V
Supramolecule | Name: MYOSIN V / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
-Macromolecule #1: Myosin-V
Macromolecule | Name: 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 |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse |
Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
Recombinant expression | Organism: Sf9 cells |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 2D array |
-Sample preparation
Buffer | Details: 20 mM Na2HPO4, 80-100 mM NaCl, 2 mM MgCl2, 1 mM ADP, 1 mM EGTA |
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Staining | Type: NEGATIVE Details: MyoV 2-D arrays were recovered from the lipid monolayer |
Grid | Details: 200 mesh copper grids covered with a reticulated carbon film. |
Vitrification | Cryogen 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 |
Details | crystals grown on a lipid-monolayer |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/ST |
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Temperature | Average: 103 K |
Date | Feb 1, 2004 |
Image recording | Category: 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 12.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 24000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 70 ° |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: protomo |
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CTF correction | Details: focus gradient correction |
Crystal parameters | Unit 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 |
-Atomic model buiding 1
Software | Name: Situs and NMFF |
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Details | Protocol: Rigid body and Normal Mode Flexible. Start with Rigid body docking by using SITUS and refine with NMFF |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation |
Output model | PDB-2dfs: |