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- PDB-8a12: Plasmodium falciparum Myosin A full-length, post-rigor state comp... -

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Basic information

Entry
Database: PDB / ID: 8a12
TitlePlasmodium falciparum Myosin A full-length, post-rigor state complexed to 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 / Knx002 / antimalarial treatment / molecular motors
Function / homology
Function and homology information


pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / 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 ...: / 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
ADENOSINE-5'-DIPHOSPHATE / Myosin essential light chain ELC / Myosin A tail domain interacting protein / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMoussaoui, D. / Robblee, J.P. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.E. / Mueller-Dieckmann, C. / Baum, J. / Robert-Paganin, 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
DepositionMay 31, 2022Deposition 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.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Myosin essential light chain ELC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4469
Polymers131,6783
Non-polymers7686
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-97 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.125, 115.140, 170.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABE

#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 NF54 / Gene: CK202_4702 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BQX1

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Non-polymers , 5 types, 501 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 277.4 K / Method: vapor diffusion
Details: 1,6 M Ammonium sulfate; 0,1 M HEPES pH 7,5; 4% PEG400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.027→85.112 Å / Num. obs: 87835 / % possible obs: 94.4 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.1
Reflection shellResolution: 2.027→2.223 Å / Rmerge(I) obs: 1.136 / Num. unique obs: 4371 / CC1/2: 0.632

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YCY

6ycy


Resolution: 2.03→42.56 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 4282 4.9 %
Rwork0.1858 83063 -
obs0.1882 87345 75.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.62 Å2 / Biso mean: 57.8874 Å2 / Biso min: 25.83 Å2
Refinement stepCycle: final / Resolution: 2.03→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8569 0 46 495 9110
Biso mean--49.71 55.48 -
Num. residues----1072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.050.175560.236482882
2.05-2.070.3106110.24651962076
2.07-2.10.3275140.25373393539
2.1-2.130.2842180.288352554314
2.13-2.150.2752390.256269873719
2.15-2.180.3276480.259489894625
2.18-2.220.2735580.2491112117031
2.22-2.250.2523760.25391535161143
2.25-2.280.2791210.23922267238863
2.28-2.320.27961650.24442929309481
2.32-2.360.32261990.24053347354693
2.36-2.40.26081920.22733594378699
2.4-2.450.29211710.224236343805100
2.45-2.50.27972020.214536153817100
2.5-2.550.24781870.215736313818100
2.55-2.610.23721800.212636423822100
2.61-2.680.23931980.215236133811100
2.68-2.750.25021650.223936823847100
2.75-2.830.29441830.228836113794100
2.83-2.920.28441850.240636383823100
2.92-3.030.31051850.22433645383099
3.03-3.150.27831800.21513612379299
3.15-3.290.26461670.20123542370996
3.29-3.470.25911460.18843270341688
3.47-3.680.24751740.176936713845100
3.68-3.970.2041960.147536873883100
3.97-4.370.17021760.1337073883100
4.37-50.18032060.132437383944100
5-6.290.20612140.180537273941100
6.29-42.560.2392200.19663876409699
Refinement TLS params.Method: refined / Origin x: 3.0918 Å / Origin y: 0.1768 Å / Origin z: 37.8024 Å
111213212223313233
T0.2836 Å2-0.0029 Å20.0003 Å2-0.257 Å20.0238 Å2--0.3155 Å2
L0.2541 °20.0032 °2-0.046 °2-0.1299 °20.1327 °2--0.7997 °2
S0.0043 Å °0.0095 Å °0.0207 Å °0.0086 Å °-0.0368 Å °0.002 Å °-0.0504 Å °-0.0186 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 903
2X-RAY DIFFRACTION1allB28 - 201
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allE2 - 201
5X-RAY DIFFRACTION1allS2 - 507

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