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- PDB-4lli: Crystal Structure of human Myosin 5a globular domain -

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Basic information

Entry
Database: PDB / ID: 4lli
TitleCrystal Structure of human Myosin 5a globular domain
ComponentsUnconventional myosin-Va
KeywordsMOTOR PROTEIN / GLOBULAR TAIL / TYPE V MYOSIN / DILUTE DOMAIN
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / actin filament-based movement / filopodium tip / vesicle transport along actin filament / myosin complex / microfilament motor activity / Insulin processing / vesicle-mediated transport ...post-Golgi vesicle-mediated transport / insulin-responsive compartment / melanosome transport / actin filament-based movement / filopodium tip / vesicle transport along actin filament / myosin complex / microfilament motor activity / Insulin processing / vesicle-mediated transport / ruffle / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / cellular response to insulin stimulus / melanosome / actin filament binding / actin cytoskeleton / protein transport / growth cone / calmodulin binding / neuron projection / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Myosin 5a, cargo-binding 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. ...Myosin 5a, cargo-binding 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Va
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsVelvarska, H. / Niessing, D.
CitationJournal: Plos One / Year: 2013
Title: Structural insights into the globular tails of the human type v myosins myo5a, myo5b, and myo5c.
Authors: Velvarska, H. / Niessing, D.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Unconventional myosin-Va
B: Unconventional myosin-Va


Theoretical massNumber of molelcules
Total (without water)90,3272
Polymers90,3272
Non-polymers00
Water6,810378
1
A: Unconventional myosin-Va


Theoretical massNumber of molelcules
Total (without water)45,1631
Polymers45,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Unconventional myosin-Va


Theoretical massNumber of molelcules
Total (without water)45,1631
Polymers45,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.057, 87.105, 130.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Unconventional myosin-Va / / Dilute myosin heavy chain / non-muscle / Myosin heavy chain 12 / Myosin-12 / Myoxin


Mass: 45163.410 Da / Num. of mol.: 2
Fragment: Myosin Va cargo binding domain, UNP residues 1467-1855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH12, MYO5A / Plasmid: pGex-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Star / References: UniProt: Q9Y4I1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.112-0.125 M succinic acid pH 7.0. 16-18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2010
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.2→43.5 Å / Num. obs: 43515 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.237 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→43.5 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 28.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.246 2234 5.13 %
Rwork0.198 --
obs0.201 43515 99.5 %
all-58577 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å / Luzzati d res low obs: 2.2 Å / Luzzati sigma a obs: 0.165 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 0 378 6438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076162
X-RAY DIFFRACTIONf_angle_d1.0238311
X-RAY DIFFRACTIONf_dihedral_angle_d15.492372
X-RAY DIFFRACTIONf_chiral_restr0.065955
X-RAY DIFFRACTIONf_plane_restr0.0041059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24780.30491320.23032551X-RAY DIFFRACTION99
2.2478-2.30010.28191570.21742502X-RAY DIFFRACTION99
2.3001-2.35760.29531480.22552531X-RAY DIFFRACTION99
2.3576-2.42140.28031270.21762565X-RAY DIFFRACTION100
2.4214-2.49260.32291550.21712514X-RAY DIFFRACTION99
2.4926-2.57310.29031480.21562533X-RAY DIFFRACTION99
2.5731-2.6650.23771210.21172596X-RAY DIFFRACTION100
2.665-2.77170.28121300.20522549X-RAY DIFFRACTION99
2.7717-2.89780.27191540.21662546X-RAY DIFFRACTION100
2.8978-3.05060.29581300.21292577X-RAY DIFFRACTION100
3.0506-3.24170.26911330.21252597X-RAY DIFFRACTION100
3.2417-3.49180.22031340.20742599X-RAY DIFFRACTION100
3.4918-3.84310.21791320.18572597X-RAY DIFFRACTION100
3.8431-4.39870.20851430.17022627X-RAY DIFFRACTION100
4.3987-5.54010.21571530.17232621X-RAY DIFFRACTION100
5.5401-43.50.20221370.1832776X-RAY DIFFRACTION99

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