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- PDB-4ll6: Structure of Myo4p globular tail domain. -

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Basic information

Entry
Database: PDB / ID: 4ll6
TitleStructure of Myo4p globular tail domain.
ComponentsMyosin-4
KeywordsMOTOR PROTEIN / Myo4p / globular tail domain / mRNA localization
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 / vesicle transport along actin filament / intracellular mRNA localization ...RHOT2 GTPase cycle / RHOT1 GTPase cycle / mating type switching / endoplasmic reticulum inheritance / RHOU GTPase cycle / cellular bud / myosin V complex / cellular bud tip / vesicle transport along actin filament / intracellular mRNA localization / 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. / IQ motif, EF-hand binding site ...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. / 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
ACETIC ACID / Myosin-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsShi, H. / Singh, N. / Esselborn, F. / Blobel, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a myosinbulletadaptor complex and pairing by cargo.
Authors: Shi, H. / Singh, N. / Esselborn, F. / Blobel, G.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8273
Polymers42,7071
Non-polymers1202
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.881, 76.363, 77.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Myosin-4 / SWI5-dependent HO expression protein 1


Mass: 42707.336 Da / Num. of mol.: 1 / Fragment: UNP residues 1098-1471 / Mutation: K1366N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MYO4, SHE1, YAL029C, FUN22 / Production host: Escherichia coli (E. coli) / References: UniProt: P32492
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% Tacsimate, 0.1M MES, pH 7.0, 25% (w/v) PEG 1K, 10mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9798, 0.9801, 0.9574
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2007
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.98011
30.95741
ReflectionResolution: 2.3→35 Å / Num. all: 17416 / Num. obs: 17120 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
CBASSdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→35 Å / σ(F): 1 / Stereochemistry target values: Maximum Likelihood
RfactorNum. reflectionSelection details
Rfree0.278 1564 RANDOM
Rwork0.225 --
obs-15738 -
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 8 93 2897
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.38

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