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- PDB-3au5: Structure of the human myosin-X MyTH4-FERM cassette -

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Basic information

Entry
Database: PDB / ID: 3au5
TitleStructure of the human myosin-X MyTH4-FERM cassette
ComponentsMyosin-X
KeywordsMOTOR PROTEIN / protein-protein interaction / motor protein cargo transportation
Function / homology
Function and homology information


plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / regulation of filopodium assembly / cytoskeleton-dependent intracellular transport / filopodium membrane / myosin complex / spectrin binding / microfilament motor activity ...plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / regulation of filopodium assembly / cytoskeleton-dependent intracellular transport / filopodium membrane / myosin complex / spectrin binding / microfilament motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / ruffle / filopodium / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / actin filament binding / lamellipodium / cell cortex / regulation of cell shape / calmodulin binding / neuron projection / neuronal cell body / nucleolus / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
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 / 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 / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / PH-like domain superfamily / Roll / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHirano, Y. / Takahashi, A. / Hakoshima, T.
CitationJournal: Embo J. / Year: 2011
Title: Structural basis of cargo recognition by the myosin-X MyTH4-FERM domain
Authors: Hirano, Y. / Hatano, T. / Takahashi, A. / Toriyama, M. / Inagaki, N. / Hakoshima, T.
History
DepositionJan 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-X
B: Myosin-X


Theoretical massNumber of molelcules
Total (without water)126,8512
Polymers126,8512
Non-polymers00
Water1,69394
1
A: Myosin-X


Theoretical massNumber of molelcules
Total (without water)63,4251
Polymers63,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myosin-X


Theoretical massNumber of molelcules
Total (without water)63,4251
Polymers63,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.565, 49.313, 158.407
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 63425.477 Da / Num. of mol.: 2 / Fragment: MyTH4-FERM cassette, UNP residues 1486-2058
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO10, KIAA0799 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q9HD67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER1663THR IS NATURAL VARIANT ACCORDING TO DATABASE Q9HD67 (MYO10_HUMAN).

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 5% MPD, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.99458 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2010 / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99458 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 42632 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.7 Å2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.29 / % possible all: 92.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AU4

3au4


Resolution: 2.55→32.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 55512.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2021 5 %RANDOM
Rwork0.236 ---
obs0.236 40247 91.9 %-
all-40247 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8321 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.39 Å20 Å22.08 Å2
2--0.12 Å20 Å2
3---6.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.55→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 0 94 7782
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 294 5.2 %
Rwork0.279 5377 -
obs-5377 78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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