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- PDB-8w41: Cryo-EM structure of Myosin VI in the autoinhibited state -

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Basic information

Entry
Database: PDB / ID: 8w41
TitleCryo-EM structure of Myosin VI in the autoinhibited state
Components
  • Calmodulin-1
  • Unconventional myosin-VI
KeywordsMOTOR PROTEIN / myosin VI / autoinhibition / intracellular transport
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 / regulation of secretion / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / minus-end directed microfilament motor activity / Ca2+ pathway / unconventional myosin complex / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / actin filament-based movement / PKA activation / Platelet degranulation / clathrin-coated vesicle membrane / inner ear auditory receptor cell differentiation / Gap junction degradation / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / vesicle transport along actin filament / Trafficking of AMPA receptors / RHOBTB1 GTPase cycle / microfilament motor activity / inner ear morphogenesis / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / filamentous actin / protein phosphatase activator activity / microvillus / cytoskeletal motor activity / RHOU GTPase cycle / adenylate cyclase binding / endocytic vesicle / catalytic complex / DNA damage response, signal transduction by p53 class mediator / detection of calcium ion / autophagosome / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / RHOBTB2 GTPase cycle / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / clathrin-coated pit / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / sperm midpiece / ruffle / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / filopodium / regulation of cytokinesis / actin filament organization / actin filament / ADP binding / spindle microtubule / sensory perception of sound / intracellular protein transport / positive regulation of receptor signaling pathway via JAK-STAT / ruffle membrane / spindle pole / cellular response to type II interferon / endocytosis / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / actin filament binding / actin cytoskeleton / apical part of cell
Similarity search - Function
: / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) ...: / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Calmodulin-1 / Unconventional myosin-VI
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsNiu, F. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
CitationJournal: Nat Commun / Year: 2024
Title: Autoinhibition and activation of myosin VI revealed by its cryo-EM structure
Authors: Niu, F. / Li, L. / Wang, L. / Xiao, J. / Xu, S. / Liu, Y. / Lin, L. / Yu, C. / Wei, Z.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Calmodulin-1
I: Calmodulin-1
A: Unconventional myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,36510
Polymers182,6583
Non-polymers7077
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 3 molecules BIA

#1: Protein Calmodulin-1 /


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calm1, Calm, Cam, Cam1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P0DP26
#2: Protein Unconventional myosin-VI /


Mass: 148952.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO6 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9UM54

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Non-polymers , 4 types, 7 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Myosin VI and CalmodulinCOMPLEX#1-#20RECOMBINANT
2myosin VICOMPLEX#21RECOMBINANT
3CalmodulinCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.4
SpecimenEmbedding 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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
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
1Topazparticle selection
2SerialEM3.7image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12RELION3.1classification
13cryoSPARC43D reconstruction
14PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10544925
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173658 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12V26

2v26

12V261PDBexperimental model
23GN4

3gn4

13GN42PDBexperimental model
36OBI

6obi

16OBI3PDBexperimental model
42N12

2n12

12N124PDBexperimental model
52KIA

2kia

12KIA5PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612061
ELECTRON MICROSCOPYf_angle_d0.73116191
ELECTRON MICROSCOPYf_dihedral_angle_d21.4221593
ELECTRON MICROSCOPYf_chiral_restr0.0471726
ELECTRON MICROSCOPYf_plane_restr0.0052128

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