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- PDB-5ejr: Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF2 domain -

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Basic information

Entry
Database: PDB / ID: 5ejr
TitleStructure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF2 domain
ComponentsMyosin-I heavy chain
KeywordsMOTOR PROTEIN / Myosin / motor myosin / myosin tail / MyTH4-FERM
Function / homology
Function and homology information


spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup ...spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup / phagocytosis / filopodium / actin filament organization / cell morphogenesis / endocytosis / : / actin filament binding / actin cytoskeleton / actin binding / cell cortex / microtubule binding / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain ...MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 / 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: 2 Å
AuthorsPlanelles-Herrero, V.J. / Sirkia, H. / Sourigues, Y. / Clause, J. / Titus, M.A. / Houdusse, A.
Funding support France, 5items
OrganizationGrant numberCountry
CNRS France
French National Research Agency France
FRM France
Ligue Nationale contre le Cancer France
ARC France
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 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 1, 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)58,7578
Polymers58,3221
Non-polymers4347
Water4,882271
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint23 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 58.950, 64.360
Angle α, β, γ (deg.)90.070, 96.780, 108.480
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 58322.457 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 (bacteria) / Variant (production host): AI / References: UniProt: Q9U1M8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 1500, 0.1M MMT (DL-Malic Acid-MES-Tris) pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36454 / % possible obs: 97.51 % / Redundancy: 2 % / Rsym value: 0.065 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.14 / % possible all: 95.07

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.1refinement
PDB_EXTRACT3.15data extraction
PHENIX2.5.6phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2→41.22 Å / Cor.coef. Fo:Fc: 0.9404 / Cor.coef. Fo:Fc free: 0.9218 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1798 4.93 %RANDOM
Rwork0.1788 ---
obs0.1808 36454 97.51 %-
Displacement parametersBiso max: 135.84 Å2 / Biso mean: 40.07 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1--4.0235 Å24.6655 Å2-1.8514 Å2
2--3.0203 Å24.4864 Å2
3---1.0032 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: final / Resolution: 2→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 30 271 4350
Biso mean--39.39 40.37 -
Num. residues----503
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1506SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes116HARMONIC2
X-RAY DIFFRACTIONt_gen_planes584HARMONIC5
X-RAY DIFFRACTIONt_it4198HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion575SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5108SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4198HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5665HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.16
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2335 119 4.11 %
Rwork0.2276 2779 -
all0.2278 2898 -
obs--97.51 %
Refinement TLS params.Method: refined / Origin x: 30.3447 Å / Origin y: -42.9024 Å / Origin z: -62.1179 Å
111213212223313233
T0.0256 Å2-0.0554 Å2-0.0035 Å2--0.0632 Å2-0.0059 Å2---0.0516 Å2
L0.1221 °20.1428 °2-0.0553 °2-0.8863 °20.271 °2--0.6407 °2
S-0.0761 Å °0.062 Å °-0.0088 Å °-0.1697 Å °0.0575 Å °0.0426 Å °0.2072 Å °-0.1175 Å °0.0187 Å °
Refinement TLS groupSelection details: { A|* }

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