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- PDB-7yv9: Cryo-EM structure of full-length Myosin Va in the autoinhibited state -

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Basic information

Entry
Database: PDB / ID: 7yv9
TitleCryo-EM structure of full-length Myosin Va in the autoinhibited state
Components
  • Calmodulin-1
  • Unconventional myosin-Va
KeywordsMOTOR PROTEIN / intracellular trafficking / molecular motor / myosin / autoinhibition
Function / homology
Function and homology information


phenol-containing compound metabolic process / 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 / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs ...phenol-containing compound metabolic process / 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 / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Calmodulin induced events / Synthesis of IP3 and IP4 in the cytosol / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Reduction of cytosolic Ca++ levels / Calcineurin activates NFAT / Ion transport by P-type ATPases / RAF activation / VEGFR2 mediated vascular permeability / Protein methylation / vesicle transport along actin filament / RAS processing / Ca2+ pathway / FCERI mediated Ca+2 mobilization / Extra-nuclear estrogen signaling / RHO GTPases activate IQGAPs / Unblocking of NMDA receptors, glutamate binding and activation / post-Golgi vesicle-mediated transport / PKA activation / secretory granule localization / RAF/MAP kinase cascade / Smooth Muscle Contraction / filopodium tip / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / actomyosin / Stimuli-sensing channels / : / Ion homeostasis / type 3 metabotropic glutamate receptor binding / myosin complex / microfilament motor activity / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / pigmentation / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / detection of calcium ion / postsynaptic cytosol / regulation of cardiac muscle contraction / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ruffle / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated potassium channel complex / calcium channel complex / secretory granule / regulation of heart rate / calyx of Held / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / response to amphetamine / sarcomere / actin filament / calcium channel regulator activity / response to calcium ion / recycling endosome / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / mitochondrial membrane / small GTPase binding / spindle pole / calcium-dependent protein binding / melanosome / late endosome / peroxisome / myelin sheath
Similarity search - Function
Myosin 5a, cargo-binding domain / : / Unconventional myosin-Va domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like ...Myosin 5a, cargo-binding domain / : / Unconventional myosin-Va 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / 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
Unconventional myosin-Va / Calmodulin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.78 Å
AuthorsNiu, F. / Wei, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131, 31870757, 32170697, 31800643 China
CitationJournal: Sci Adv / Year: 2022
Title: Autoinhibition and activation mechanisms revealed by the triangular-shaped structure of myosin Va.
Authors: Fengfeng Niu / Yong Liu / Kang Sun / Shun Xu / Jiayuan Dong / Cong Yu / Kaige Yan / Zhiyi Wei /
Abstract: As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and ...As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and autoinhibited state, which can be relieved by cargo binding. The molecular mechanisms governing the autoinhibition and activation of MyoVa remain unclear. Here, we report the cryo-electron microscopy structure of the two full-length, closed MyoVa heavy chains in complex with 12 calmodulin light chains at 4.78-Å resolution. The MyoVa adopts a triangular structure with multiple intra- and interpolypeptide chain interactions in establishing the closed state with cargo binding and adenosine triphosphatase activity inhibited. Structural, biochemical, and cellular analyses uncover an asymmetric autoinhibition mechanism, in which the cargo-binding sites in the two MyoVa heavy chains are differently protected. Thus, specific and efficient MyoVa activation requires coincident binding of multiple cargo adaptors, revealing an intricate and elegant activity regulation of the motor in response to cargos.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-Va
B: Calmodulin-1
C: Calmodulin-1
D: Calmodulin-1
E: Calmodulin-1
F: Calmodulin-1
G: Calmodulin-1
H: Unconventional myosin-Va
I: Calmodulin-1
J: Calmodulin-1
K: Calmodulin-1
L: Calmodulin-1
M: Calmodulin-1
N: Calmodulin-1
X: Unconventional myosin-Va
Y: Unconventional myosin-Va


Theoretical massNumber of molelcules
Total (without water)1,052,81316
Polymers1,052,81316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Unconventional myosin-Va


Mass: 212657.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo5a / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3YZ62
#2: Protein
Calmodulin-1


Mass: 16848.605 Da / Num. of mol.: 12 / Mutation: E32Q,E68Q,E105Q,E141Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calm1, Calm, Cam, Cam1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DP26

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Myosin Va and Calmodulin complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.63 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
280 mMsodium chlorideNaCl1
32 mMmagnesium chlorideMgCl21
41 mMEGTAC14H24N2O101
51 mMDTTC4H10O2S21
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCV3.1.0particle selection
2SerialEM3.7image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.16model fitting
8Coot0.9.4model fitting
10cryoSPARCV3.1.0initial Euler assignment
11cryoSPARCV3.1.0final Euler assignment
12cryoSPARCV3.1.0classification
13cryoSPARCV3.1.03D reconstruction
14PHENIX1.18.2model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 20747000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160273 / Symmetry type: POINT
Atomic model buildingB value: 167.3 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11OE9

1oe9

11OE91PDBexperimental model
23WB8

3wb8

13WB82PDBexperimental model
32IX7

2ix7

12IX73PDBexperimental model

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