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- PDB-6eyw: Structure of Yeast Myosin 5 Cargo Binding Domain in Trigonal Spac... -

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Basic information

Entry
Database: PDB / ID: 6eyw
TitleStructure of Yeast Myosin 5 Cargo Binding Domain in Trigonal Space Group
ComponentsMyosin-2
KeywordsTRANSPORT PROTEIN / Myosin V Globular Tail Domain Rab GTPases vesicle trafficking yeast myosin
Function / homology
Function and homology information


peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance ...peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site / cellular bud tip / vesicle transport along actin filament / cellular bud neck / mating projection tip / fungal-type vacuole membrane / vesicle docking involved in exocytosis / microfilament motor activity / intracellular distribution of mitochondria / filamentous actin / actin filament bundle / establishment of mitotic spindle orientation / vesicle-mediated transport / transport vesicle / actin filament organization / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / ATP binding / membrane / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsTan, J. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/1A/1239 Ireland
CitationJournal: To Be Published
Title: Structure of yeast myosin V cargo binding domain in a new trigonal space group
Authors: Tan, J. / Khan, A.R.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.2Jan 17, 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
X: Myosin-2


Theoretical massNumber of molelcules
Total (without water)48,8021
Polymers48,8021
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 63.830, 227.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Myosin-2 / Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain ...Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2


Mass: 48801.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MYO2, CDC66, YOR326W, O6167 / Production host: Escherichia coli (E. coli) / References: UniProt: P19524
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3000 0.1M Tris-Cl, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.88→49.7 Å / Num. obs: 12921 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.119 / Net I/σ(I): 14
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 6 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.638 / Rrim(I) all: 0.992 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2f6h

2f6h


Resolution: 2.88→49.726 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1271 10.03 %
Rwork0.2193 --
obs0.2244 12671 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→49.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 0 4 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083164
X-RAY DIFFRACTIONf_angle_d1.2544295
X-RAY DIFFRACTIONf_dihedral_angle_d15.8521165
X-RAY DIFFRACTIONf_chiral_restr0.264508
X-RAY DIFFRACTIONf_plane_restr0.004533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8801-2.99540.44851410.34591262X-RAY DIFFRACTION100
2.9954-3.13170.34531420.28271231X-RAY DIFFRACTION99
3.1317-3.29670.32341410.26161247X-RAY DIFFRACTION99
3.2967-3.50320.34451340.24681255X-RAY DIFFRACTION98
3.5032-3.77370.31191390.27061263X-RAY DIFFRACTION98
3.7737-4.15320.25431380.19811239X-RAY DIFFRACTION98
4.1532-4.75380.22651400.17571270X-RAY DIFFRACTION98
4.7538-5.98770.25531440.1851260X-RAY DIFFRACTION96
5.9877-49.73380.19931520.1961373X-RAY DIFFRACTION97

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