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

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Basic information

Entry
Database: PDB / ID: 8cdm
TitlePlasmodium falciparum Myosin A full-length, post-rigor state complexed to the inhibitor KNX-002
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 / inner membrane pellicle complex / glideosome / myosin complex / myosin II complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin complex / myosin II 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Kinesin motor domain superfamily / : ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / 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
Chem-KQ0 / Myosin essential light chain ELC / Calmodulin / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMoussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.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 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 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)132,3227
Polymers131,6783
Non-polymers6444
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-37 kcal/mol
Surface area48710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.931, 114.409, 170.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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

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Non-polymers , 4 types, 360 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.6 Å3/Da / Density % sol: 65.79 %
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: 1.0722 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.35→94.97 Å / Num. obs: 55344 / % possible obs: 93.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 55.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.3
Reflection shellResolution: 2.35→2.53 Å / Rmerge(I) obs: 1.672 / Num. unique obs: 2767 / CC1/2: 0.578

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YCY

6ycy


Resolution: 2.35→46.44 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 2810 5.08 %
Rwork0.1964 52524 -
obs0.199 55334 75.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.72 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8537 0 44 356 8937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778738
X-RAY DIFFRACTIONf_angle_d0.923911775
X-RAY DIFFRACTIONf_chiral_restr0.05371326
X-RAY DIFFRACTIONf_plane_restr0.0071503
X-RAY DIFFRACTIONf_dihedral_angle_d5.51761168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.2818150.3008265X-RAY DIFFRACTION7.8
2.4-2.440.3703280.2838513X-RAY DIFFRACTION14.94
2.44-2.490.2788410.2604866X-RAY DIFFRACTION25.19
2.49-2.540.3049590.25231209X-RAY DIFFRACTION34.84
2.54-2.590.2431060.25041528X-RAY DIFFRACTION45.21
2.59-2.650.3136840.24821837X-RAY DIFFRACTION52.96
2.65-2.720.26421240.24632093X-RAY DIFFRACTION61.09
2.72-2.790.2741420.24912546X-RAY DIFFRACTION73.62
2.79-2.870.28691840.24453191X-RAY DIFFRACTION92.57
2.87-2.970.32542050.25623382X-RAY DIFFRACTION99.34
2.97-3.070.281700.22993461X-RAY DIFFRACTION99.4
3.07-3.20.2631850.2063435X-RAY DIFFRACTION99.04
3.2-3.340.2751650.20413483X-RAY DIFFRACTION99.62
3.34-3.520.24921950.18693431X-RAY DIFFRACTION99.32
3.52-3.740.2621860.19023505X-RAY DIFFRACTION99.51
3.74-4.030.2221690.16693492X-RAY DIFFRACTION99.62
4.03-4.430.20551880.16053488X-RAY DIFFRACTION99.65
4.43-5.070.21781870.16093529X-RAY DIFFRACTION99.73
5.07-6.390.24211720.21383593X-RAY DIFFRACTION99.71
6.39-46.440.25162050.20373677X-RAY DIFFRACTION99.06
Refinement TLS params.Method: refined / Origin x: 2.97217217614 Å / Origin y: 0.433284134512 Å / Origin z: 37.62087237 Å
111213212223313233
T0.337845738443 Å20.00264444608135 Å20.0154784857095 Å2-0.234802224707 Å20.0235658781966 Å2--0.373457347196 Å2
L0.409795373218 °2-0.00895175884698 °20.00205876985858 °2-0.261917626849 °20.148118517878 °2--1.11023997242 °2
S-0.014977625302 Å °-0.0178725577582 Å °0.0257693026734 Å °0.0246950545584 Å °-0.0226256686072 Å °0.0232376383163 Å °-0.068717834945 Å °0.0279193653492 Å °0.0446726368044 Å °
Refinement TLS groupSelection details: all

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