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- PDB-5kg8: Rigor myosin X co-complexed with an actin filament -

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Basic information

Entry
Database: PDB / ID: 5kg8
TitleRigor myosin X co-complexed with an actin filament
Components
  • Actin, alpha skeletal muscle
  • Unconventional myosin-X
KeywordsMOTOR PROTEIN / myosin molecular motors cytoskeletal motility
Function / homology
Function and homology information


plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / cytoskeleton-dependent intracellular transport / filopodium tip / regulation of filopodium assembly / filopodium membrane / myosin complex / cytoskeletal motor activator activity / spectrin binding ...plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / cytoskeleton-dependent intracellular transport / filopodium tip / regulation of filopodium assembly / filopodium membrane / myosin complex / cytoskeletal motor activator activity / spectrin binding / myosin heavy chain binding / microfilament motor activity / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / phosphatidylinositol-3,4,5-trisphosphate binding / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / ruffle / actin filament polymerization / FCGR3A-mediated phagocytosis / actin filament / filopodium / Regulation of actin dynamics for phagocytic cup formation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / regulation of cell shape / lamellipodium / cell body / cell cortex / calmodulin binding / neuron projection / hydrolase activity / protein domain specific binding / neuronal cell body / calcium ion binding / positive regulation of gene expression / nucleolus / magnesium ion binding / signal transduction / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain ...Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / Ras-associating (RA) domain / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / ATPase, nucleotide binding domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsSindelar, C.V. / Houdusse, A. / Sweeney, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 110530-01 United States
CitationJournal: Nat Commun / Year: 2016
Title: The myosin X motor is optimized for movement on actin bundles.
Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun ...Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun Park / Olena Pylypenko / Marco Cecchini / Charles V Sindelar / H Lee Sweeney / Anne Houdusse /
Abstract: Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and ...Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and some pathogenic infections. By determining high-resolution structures of key components of this motor, and characterizing the in vitro behaviour of the native dimer, we identify the features that explain the myosin X dimer behaviour. Single-molecule studies demonstrate that a native myosin X dimer moves on actin bundles with higher velocities and takes larger steps than on single actin filaments. The largest steps on actin bundles are larger than previously reported for artificially dimerized myosin X constructs or any other myosin. Our model and kinetic data explain why these large steps and high velocities can only occur on bundled filaments. Thus, myosin X functions as an antiparallel dimer in cells with a unique geometry optimized for movement on actin bundles.
History
DepositionJun 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Unconventional myosin-X
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle


Theoretical massNumber of molelcules
Total (without water)210,5664
Polymers210,5664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Unconventional myosin-X / Unconventional myosin-10


Mass: 85083.086 Da / Num. of mol.: 1 / Fragment: motor domain (UNP residues 3-741)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO10, KIAA0799 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD67
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41827.609 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Actin filament decorated by the myosin X motor domain / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: MULTIPLE SOURCES
Buffer solutionpH: 6.8
Buffer componentConc.: 5 mM / Name: MOPS
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 26780 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1438 nm / Calibrated defocus max: 5251 nm / Cs: 2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 13 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 154

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Processing

EM software
IDNameVersionCategoryDetails
1boxerparticle selectionEMAN boxer was used to manually select filaments.
2SerialEMimage acquisition
4CTFFIND3CTF correction
10SPARXinitial Euler assignmentsxihrsr was used on binned copies of the boxed filaments.
11FREALIGN8.06final Euler assignment
13FREALIGN8.063D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 167.1 ° / Axial rise/subunit: 27.44 Å / Axial symmetry: C1 / Details: Not directly applicable to the modeled coordinates
3D reconstructionResolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57927 / Algorithm: FOURIER SPACE
Details: Symmetry was not applied in this reconstruction. The provided symmetry parameters are nominal, and were not actually used.
Num. of class averages: 1 / Symmetry type: HELICAL

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