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

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Basic information

Entry
Database: PDB / ID: 2dfs
Title3-D structure of Myosin-V inhibited state
Components
  • Calmodulin
  • Myosin-5A
KeywordsCONTRACTILE PROTEIN/TRANSPORT PROTEIN / myosin-V / inhibited state / calmodulin / cryoelectron tomography / CONTRACTILE PROTEIN-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of calcium ion transmembrane transporter activity / 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 / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation ...negative regulation of calcium ion transmembrane transporter activity / 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 / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Reduction of cytosolic Ca++ levels / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / Calcineurin activates NFAT / Ion transport by P-type ATPases / RAF activation / minus-end directed microfilament motor activity / VEGFR2 mediated vascular permeability / RAS processing / Ca2+ pathway / insulin-responsive compartment / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Smooth Muscle Contraction / : / : / : / : / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / : / Stimuli-sensing channels / establishment of protein localization to mitochondrial membrane / Ion homeostasis / type 3 metabotropic glutamate receptor binding / myosin complex / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / microfilament motor activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / filamentous actin / calcineurin-mediated signaling / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / catalytic complex / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / postsynaptic cytosol / activation of adenylate cyclase activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / vesicle-mediated transport / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / regulation of heart rate / calyx of Held / actin filament organization / response to amphetamine / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / regulation of cytokinesis / protein localization to plasma membrane / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium-mediated signaling / response to calcium ion / mitochondrial membrane / cellular response to type II interferon
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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / 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 speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodELECTRON CRYSTALLOGRAPHY / electron tomography / Resolution: 24 Å
AuthorsLiu, J. / Taylor, D.W. / Krementsova, E.B. / Trybus, K.M. / Taylor, K.A.
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 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Myosin-5A
B: Calmodulin
C: Calmodulin
D: Calmodulin
E: Calmodulin
F: Calmodulin
G: Calmodulin
M: Myosin-5A
N: Calmodulin
O: Calmodulin
P: Calmodulin
Q: Calmodulin
R: Calmodulin
S: Calmodulin


Theoretical massNumber of molelcules
Total (without water)453,48814
Polymers453,48814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)653.000, 653.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Myosin-5A / Myosin Va / Dilute myosin heavy chain / non-muscle / Myosin heavy chain p190 / Myosin-V


Mass: 126415.695 Da / Num. of mol.: 2 / Fragment: residues 1-1080
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02440
#2: Protein
Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62204, UniProt: P0DP26*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: TISSUE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: Myosin-V / Type: TISSUE / Details: myosin-V inhibited state
Buffer solutionName: 20mM Na2HPO4, 80-100mM NaCl, 2mM MgCl2, 1mM ADP, 1mM EGTA, 8-9% PEG 8000
Details: 20mM Na2HPO4, 80-100mM NaCl, 2mM MgCl2, 1mM ADP, 1mM EGTA, 8-9% PEG 8000
SpecimenConc.: 0.2 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: 200 mesh copper grids covered with a reticulated carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: liquid ethane

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Data collection

MicroscopyModel: FEI/PHILIPS CM300FEG/ST / Date: Feb 1, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 24000 X / Calibrated magnification: 24000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 12000 nm / Cs: 2 mm
Specimen holderTemperature: 103 K / Tilt angle max: 70 ° / Tilt angle min: -70 °
Image recordingElectron dose: 30 e/Å2 / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Details: 2048x2048
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1NMFFmodel fitting
2Situsmodel fitting
3PROTOMO3D reconstruction
CTF correctionDetails: CTF gradient correction
3D reconstructionMethod: electron tomography and 3-D average / Resolution: 24 Å / Num. of particles: 4029 / Nominal pixel size: 5.56 Å / Actual pixel size: 5.56 Å
Details: Tilt series images were aligned using marker-free alignment. Molecular volumes extracted from the cryotomograms, aligned in 3-D. Marker-free alignment is described in the reference: ...Details: Tilt series images were aligned using marker-free alignment. Molecular volumes extracted from the cryotomograms, aligned in 3-D. Marker-free alignment is described in the reference: Winkler,H. and Taylor,K.A. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy, 106, 240-254 (2006)
Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross correlation
Details: METHOD--Rigid body docking first and then refined with normal mode flexible fitting. REFINEMENT PROTOCOL--Rigid body docking and normal mode flexible fitting. For the fitting the density ...Details: METHOD--Rigid body docking first and then refined with normal mode flexible fitting. REFINEMENT PROTOCOL--Rigid body docking and normal mode flexible fitting. For the fitting the density corresponding to the two myosin V heads within the asymmetric unit was segmented from the rest of the map using the watershed transform (Volkman 2002. J.STRUCT.BIOL. 138, 123-129). After fitting the atomic model against the head density, the coordinates were not refined further against the nearest neighbor myosin V heads to remove bad crystal contacts. The alpha-helical coiled-coil domain was manually fit to the and not refined further.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11W7I

1w7i

11W7I1PDBexperimental model
21N2D

1n2d

11N2D2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms29614 0 0 0 29614

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