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- PDB-8cdq: Plasmodium falciparum Myosin A full-length, post-rigor state comp... -

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Basic information

Entry
Database: PDB / ID: 8cdq
TitlePlasmodium falciparum Myosin A full-length, post-rigor state complexed to the inhibitor KNX-002 and Mg.ATP-gamma-S
Components
  • Myosin A tail domain interacting protein
  • Myosin essential light chain ELC
  • Myosin-A
KeywordsMOTOR PROTEIN / Malaria / Plasmodium falciparum / Myosin A / KNX-002 / antimalarial treatment / molecular motors
Function / homology
Function and homology information


pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity ...pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand calcium-binding domain profile. ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chem-KQ0 / Myosin A tail domain interacting protein / Myosin-A / Myosin essential light chain ELC
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMoussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.E. / Schaletzky, J. / Wehri, E. / Mueller-Dieckmann, C. ...Moussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.E. / Schaletzky, J. / Wehri, E. / Mueller-Dieckmann, C. / Baum, J. / Trybus, K.M. / Houdusse, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI 132378 United States
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of small molecule inhibition of Plasmodium falciparum myosin A informs antimalarial drug design.
Authors: Moussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / Macfarlane, J.E. / Schaletzky, J. / Wehri, E. / Mueller-Dieckmann, C. / Baum, J. / Trybus, K.M. / Houdusse, A.
History
DepositionJan 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-A
B: Myosin A tail domain interacting protein
C: Myosin essential light chain ELC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,43015
Polymers131,6783
Non-polymers1,75212
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-78 kcal/mol
Surface area48220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.416, 170.919, 90.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Myosin-A / PfMyoA


Mass: 92474.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: MyoA, PF13_0233, PF3D7_1342600 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDR3
#2: Protein Myosin A tail domain interacting protein


Mass: 23510.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_1246400 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4W8
#3: Protein Myosin essential light chain ELC


Mass: 15692.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_1017500 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IJM4

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Non-polymers , 8 types, 317 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-KQ0 / 1-(4-methoxyphenyl)-~{N}-[(3-thiophen-2-yl-1~{H}-pyrazol-4-yl)methyl]cyclopropan-1-amine


Mass: 325.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3OS / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 63.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.0 M ammonium sulfate, 0.1M sodium HEPES pH 7,5, 4% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9687 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.21→95.08 Å / Num. obs: 57115 / % possible obs: 93.9 % / Redundancy: 7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.199 / Net I/σ(I): 8.1
Reflection shellResolution: 2.21→2.43 Å / Rmerge(I) obs: 1.476 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2857 / CC1/2: 0.546 / % possible all: 59.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YCY

6ycy


Resolution: 2.21→95.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 2834 4.96 %
Rwork0.1882 --
obs0.1905 57094 63.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→95.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8564 0 110 305 8979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098839
X-RAY DIFFRACTIONf_angle_d0.9811915
X-RAY DIFFRACTIONf_dihedral_angle_d8.1681192
X-RAY DIFFRACTIONf_chiral_restr0.0531336
X-RAY DIFFRACTIONf_plane_restr0.0071513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.250.373710.305839X-RAY DIFFRACTION1
2.25-2.290.499120.3151222X-RAY DIFFRACTION5
2.29-2.330.3062270.2641439X-RAY DIFFRACTION11
2.33-2.380.2668430.2702805X-RAY DIFFRACTION19
2.38-2.430.3887640.29411373X-RAY DIFFRACTION33
2.43-2.490.3691910.27771805X-RAY DIFFRACTION43
2.49-2.550.33861160.27292059X-RAY DIFFRACTION49
2.55-2.620.30971000.27612338X-RAY DIFFRACTION55
2.62-2.70.32321370.27192604X-RAY DIFFRACTION62
2.7-2.790.33361450.26912804X-RAY DIFFRACTION67
2.79-2.880.28191400.26543149X-RAY DIFFRACTION74
2.89-30.2881850.24583326X-RAY DIFFRACTION79
3-3.140.2822030.23413574X-RAY DIFFRACTION85
3.14-3.30.28571870.21493938X-RAY DIFFRACTION92
3.3-3.510.25762400.19594144X-RAY DIFFRACTION98
3.51-3.780.21992330.17514236X-RAY DIFFRACTION100
3.78-4.160.2022200.14864278X-RAY DIFFRACTION100
4.16-4.760.18112120.13194308X-RAY DIFFRACTION100
4.76-60.19792180.16234338X-RAY DIFFRACTION100
6-95.080.20932600.17564481X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.2041 Å / Origin y: -48.1242 Å / Origin z: 2.7952 Å
111213212223313233
T0.1388 Å20.0318 Å20.0096 Å2-0.2397 Å20.0153 Å2--0.1777 Å2
L0.3676 °20.1337 °20.0203 °2-1.26 °20.0096 °2--0.3929 °2
S-0.0203 Å °-0.0005 Å °0.0444 Å °0.0002 Å °0.0462 Å °-0.0714 Å °-0.0071 Å °0.0256 Å °-0.0253 Å °
Refinement TLS groupSelection details: all

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