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- PDB-5ejy: Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 domain -

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Basic information

Entry
Database: PDB / ID: 5ejy
TitleStructure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 domain
ComponentsMyosin-I heavy chain
KeywordsMOTOR PROTEIN / Molecular motor / myosin / myosin tail / MyTH4-FERM
Function / homology
Function and homology information


spore germination / filopodium tip / actin filament-based movement / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytosis ...spore germination / filopodium tip / actin filament-based movement / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytosis / phagocytic cup / actin filament organization / filopodium / endocytosis / cell morphogenesis / actin filament binding / actin cytoskeleton / actin binding / cell cortex / microtubule binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / DdMyo7 FERM domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / IRS-type PTB domain ...: / DdMyo7 FERM domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Variant SH3 domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-I heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSirigu, S. / Titus, M.A. / Houdusse, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Myosin MyTH4-FERM structures highlight important principles of convergent evolution.
Authors: Planelles-Herrero, V.J. / Blanc, F. / Sirigu, S. / Sirkia, H. / Clause, J. / Sourigues, Y. / Johnsrud, D.O. / Amigues, B. / Cecchini, M. / Gilbert, S.P. / Houdusse, A. / Titus, M.A.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
A: Myosin-I heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5685
Polymers57,4381
Non-polymers3,1314
Water9,062503
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.210, 90.540, 148.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin-I heavy chain / Class VII unconventional myosin / DdMVII / DdM7


Mass: 57437.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: myoI, DDB_G0274455 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: Q9U1M8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 18% PEG 8000, 100 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 69695 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rsym value: 0.057 / Net I/σ(I): 18.36
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 5.14 % / Mean I/σ(I) obs: 2.27 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pvl

3pvl


Resolution: 1.9→43.308 Å / FOM work R set: 0.8307 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 3235 5 %
Rwork0.1944 61442 -
obs0.1962 64677 99.69 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.354 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 36.31 Å2 / Biso min: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1-9.5151 Å20 Å2-0 Å2
2--2.0941 Å20 Å2
3----11.6092 Å2
Refinement stepCycle: final / Resolution: 1.9→43.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 35 503 4455
Biso mean--49.3 42.7 -
Num. residues----500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074034
X-RAY DIFFRACTIONf_angle_d0.9665448
X-RAY DIFFRACTIONf_chiral_restr0.07610
X-RAY DIFFRACTIONf_plane_restr0.004700
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411496
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 (%)
1.9-1.96790.32313180.271860386356100
1.9679-2.04670.26353200.235660666386100
2.0467-2.13990.2543200.21260826402100
2.1399-2.25270.22223210.202260896410100
2.2527-2.39380.24723200.203160946414100
2.3938-2.57860.26223220.204261176439100
2.5786-2.83810.21643230.196661336456100
2.8381-3.24860.24633250.201161686493100
3.2486-4.09240.20153280.179162386566100
4.0924-43.31930.21763380.17836417675599

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