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- PDB-4ll8: Complex of carboxy terminal domain of Myo4p and She3p middle fragment -

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Basic information

Entry
Database: PDB / ID: 4ll8
TitleComplex of carboxy terminal domain of Myo4p and She3p middle fragment
Components
  • Myosin-4
  • SWI5-dependent HO expression protein 3
KeywordsMOTOR PROTEIN/Transport Protein / Myo4p / She3p / myosin motor-adaptor complex / mRNA translocation / MOTOR PROTEIN-Transport Protein complex
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 / sequence-specific mRNA binding / microfilament motor activity / filamentous actin / mRNA transport / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / mRNA binding / endoplasmic reticulum membrane / mitochondrion / ATP binding / membrane / cytoplasm
Similarity search - Function
SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 3 / 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. ...SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 3 / 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
Myosin-4 / SWI5-dependent HO expression protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.578 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 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
E: SWI5-dependent HO expression protein 3
B: SWI5-dependent HO expression protein 3


Theoretical massNumber of molelcules
Total (without water)115,8933
Polymers115,8933
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-95 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.013, 38.116, 183.991
Angle α, β, γ (deg.)90.00, 125.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 61560.770 Da / Num. of mol.: 1 / Fragment: UNP P32492 residues 918-1073, 1089-1471 / Mutation: K1018A, K1019A, K1020A, C1113S, C1288S, C1320S
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: Protein SWI5-dependent HO expression protein 3


Mass: 27166.123 Da / Num. of mol.: 2 / Fragment: UNP P38272 residues 81-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SHE3, YBR130C, YBR1005 / Production host: Escherichia coli (E. coli) / References: UniProt: P38272
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, pH 7.0, 8% Tacsimate, 12% (w/v) PEG 3350, 0.01M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.578→50 Å / Num. obs: 18820 / % possible obs: 99.8 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.578→50 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 2522 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1644 7.3 %Random
Rwork0.2239 13210 --
obs-14616 75.5 %-
Solvent computationBsol: 36.5328 Å2
Displacement parametersBiso max: 198.03 Å2 / Biso mean: 108.3049 Å2 / Biso min: 4.03 Å2
Baniso -1Baniso -2Baniso -3
1-37.71 Å20 Å23.59 Å2
2---3.621 Å20 Å2
3----34.089 Å2
Refinement stepCycle: LAST / Resolution: 3.578→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 0 0 5337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.574
X-RAY DIFFRACTIONc_mcbond_it6.7731.5
X-RAY DIFFRACTIONc_scbond_it9.1072
X-RAY DIFFRACTIONc_mcangle_it10.752
X-RAY DIFFRACTIONc_scangle_it13.6052.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.578-3.690.4587520.40976882043
3.69-3.830.33661240.36351032115660
3.83-4.010.28671140.28141033114761.8
4.01-4.220.27891550.22271233138871
4.22-4.480.22951250.18291337146278.6
4.48-4.830.23581420.17551502164484.1
4.83-5.320.23611560.16871489164585.6
5.32-6.080.32691550.24391446160183.2
6.08-7.660.36261870.25441592177989
7.66-500.21481960.19771778197496

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