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- PDB-5hmo: myosin X motor activity -

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Basic information

Entry
Database: PDB / ID: 5hmo
Titlemyosin X motor activity
ComponentsUnconventional myosin-X
KeywordsMOTOR PROTEIN / myosin
Function / homology
Function and homology information


plus-end directed microfilament motor activity / filopodium tip / regulation of filopodium assembly / cytoskeleton-dependent intracellular transport / filopodium membrane / myosin complex / microfilament motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / ruffle / filopodium ...plus-end directed microfilament motor activity / filopodium tip / regulation of filopodium assembly / cytoskeleton-dependent intracellular transport / filopodium membrane / myosin complex / microfilament motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / ruffle / filopodium / actin filament binding / lamellipodium / cell cortex / regulation of cell shape / calmodulin binding / signal transduction / ATP binding / 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 / MyTH4 domain profile. ...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 / Ras association (RalGDS/AF-6) 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-X
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.493 Å
AuthorsRopars, V. / Blanc, F. / Samazan, F. / Houdusse, A.
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
DepositionJan 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-X
C: Unconventional myosin-X


Theoretical massNumber of molelcules
Total (without water)33,3692
Polymers33,3692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-14 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.810, 69.810, 236.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 16684.678 Da / Num. of mol.: 2 / Fragment: SAH domain and coiled-coil, UNP residues 797-926
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: MYO10 / Plasmid: pPROEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P79114

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, Ammonium citrate, dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.49→49.37 Å / Num. obs: 7979 / % possible obs: 99.8 % / Redundancy: 13.7 % / Rsym value: 0.1076 / Net I/σ(I): 15.74
Reflection shellResolution: 3.49→3.7 Å / Redundancy: 2.08 % / Mean I/σ(I) obs: 2.02 / Rsym value: 1.819 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LW9

2lw9


Resolution: 3.493→45.5 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 56.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4371 398 5.01 %
Rwork0.3914 7540 -
obs0.3938 7938 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 255.39 Å2 / Biso mean: 193.0521 Å2 / Biso min: 123.55 Å2
Refinement stepCycle: final / Resolution: 3.493→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 0 0 1946
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121946
X-RAY DIFFRACTIONf_angle_d1.8692596
X-RAY DIFFRACTIONf_chiral_restr0.07286
X-RAY DIFFRACTIONf_plane_restr0.007362
X-RAY DIFFRACTIONf_dihedral_angle_d26.931782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4926-3.99770.51831280.470124252553
3.9977-5.03560.41941300.385324812611
5.0356-45.56260.42841400.375226342774
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.74710.1318-0.71350.051-0.17320.7633-0.0116-0.37330.0215-0.2459-0.1752-0.0644-0.5258-0.20870.1869-0.32910.020.15640.3237-0.11690.12936.7177-10.6307-24.466
27.8534-3.09531.34631.6278-0.08750.83550.00270.535-0.06980.0708-0.0166-0.2031-0.14590.1190.0139-0.3099-0.11920.14430.3240.15130.2828-91.3345-8.2326-13.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN C

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