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- PDB-3mmi: Crystal structure of the globular tail of Myo4p -

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Basic information

Entry
Database: PDB / ID: 3mmi
TitleCrystal structure of the globular tail of Myo4p
ComponentsMyosin-4
KeywordsMOTOR PROTEIN / globular tail / type V myosin / dilute domain
Function / homology
Function and homology information


RHOT2 GTPase cycle / RHOT1 GTPase cycle / mating type switching / endoplasmic reticulum inheritance / RHOU GTPase cycle / cellular bud / myosin V complex / cellular bud tip / intracellular mRNA localization / vesicle transport along actin filament ...RHOT2 GTPase cycle / RHOT1 GTPase cycle / mating type switching / endoplasmic reticulum inheritance / RHOU GTPase cycle / cellular bud / myosin V complex / cellular bud tip / intracellular mRNA localization / vesicle transport along actin filament / microfilament motor activity / filamentous actin / mRNA transport / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / mitochondrion / ATP binding / membrane / cytoplasm
Similarity search - Function
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 ...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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHeuck, A. / Niessing, D.
CitationJournal: J.Cell Biol. / Year: 2010
Title: The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.
Authors: Heuck, A. / Fetka, I. / Brewer, D.N. / Huls, D. / Munson, M. / Jansen, R.P. / Niessing, D.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Myosin-4
B: Myosin-4


Theoretical massNumber of molelcules
Total (without water)87,9742
Polymers87,9742
Non-polymers00
Water3,063170
1
A: Myosin-4


Theoretical massNumber of molelcules
Total (without water)43,9871
Polymers43,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-4


Theoretical massNumber of molelcules
Total (without water)43,9871
Polymers43,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.476, 120.989, 157.683
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 Myosin-4 / SWI5-dependent HO expression protein 1 / YAL029C


Mass: 43986.934 Da / Num. of mol.: 2 / Fragment: Myo4p globular tail (UNP residues 1091-1471)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FUN22, MYO4, SHE1, YAL029C / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3* / References: UniProt: P32492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM HEPES, 20% PEG 3350, 150mM HCO2Na, 10 mM K2Pt(CN)4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→96 Å / Num. obs: 35353 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.16
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5400 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→30.51 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.532 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.348 / ESU R Free: 0.244
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1855 5 %RANDOM
Rwork0.254 ---
obs0.254 35353 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 0 170 5623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0225273
X-RAY DIFFRACTIONr_angle_refined_deg2.171.9637157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8425664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.15725.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58315868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1541510
X-RAY DIFFRACTIONr_chiral_restr0.1650.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213868
X-RAY DIFFRACTIONr_mcbond_it2.27223333
X-RAY DIFFRACTIONr_mcangle_it3.69835363
X-RAY DIFFRACTIONr_scbond_it5.2214.51940
X-RAY DIFFRACTIONr_scangle_it7.39661794
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 144 -
Rwork0.307 2543 -
obs--99.33 %

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