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- PDB-4pjk: Dicty myosin II R238E.E459R mutant (with ADP.Pi) in the Pi releas... -

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Basic information

Entry
Database: PDB / ID: 4pjk
TitleDicty myosin II R238E.E459R mutant (with ADP.Pi) in the Pi release state
ComponentsMyosin-2 heavy chain
KeywordsMOTOR PROTEIN / MOTOR DOMAIN MUTANT
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / muscle contraction / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsIsabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A.
Funding support France, United States, 3items
OrganizationGrant numberCountry
French National Research AgencyBLAN07 France
French National Research AgencyBLAN10 France
National Institutes of HealthRO01DC009100 United States
CitationJournal: Dev.Cell / Year: 2015
Title: How actin initiates the motor activity of Myosin.
Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,06512
Polymers87,7791
Non-polymers1,28611
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-33 kcal/mol
Surface area32030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 150.150, 154.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1260-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin-2 heavy chain / Myosin II heavy chain


Mass: 87779.164 Da / Num. of mol.: 1 / Mutation: R238E, E459R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhcA, DDB_G0286355 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08799, EC: 3.6.4.1

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11,25% PEG8k, 100mM MOPS pH 7,5, 1mM TCEP, 250mM MgCl2, 50mM NaH2PO4
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2010
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 55100 / % possible obs: 99.9 % / Redundancy: 7.41 % / Biso Wilson estimate: 44.17 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.64
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.99 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VOM

1vom


Resolution: 2.15→43.55 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2755 5 %RANDOM
Rwork0.1764 ---
obs0.1782 55100 99.89 %-
Displacement parametersBiso mean: 54.83 Å2
Baniso -1Baniso -2Baniso -3
1--7.8316 Å20 Å20 Å2
2---3.8868 Å20 Å2
3---11.7184 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: 1 / Resolution: 2.15→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 80 380 6050
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037814HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2003SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it5773HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion17.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion761SEMIHARMONIC5
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_contact6872SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2444 201 5 %
Rwork0.2268 3820 -
all0.2277 4021 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 21.8624 Å / Origin y: -37.3209 Å / Origin z: 29.2205 Å
111213212223313233
T-0.1582 Å20.0175 Å2-0.0343 Å2--0.0776 Å2-0.0121 Å2---0.1477 Å2
L0.4964 °2-0.0621 °20.0652 °2-0.6554 °2-0.2312 °2--1.5553 °2
S0.0594 Å °0.028 Å °0.0696 Å °-0.0771 Å °0.0159 Å °-0.0247 Å °0.2419 Å °0.1327 Å °-0.0754 Å °
Refinement TLS groupSelection details: { A|* }

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