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- PDB-6ycy: Plasmodium falciparum Myosin A full-length, post-rigor state -

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Basic information

Entry
Database: PDB / ID: 6ycy
TitlePlasmodium falciparum Myosin A full-length, post-rigor state
Components
  • Myosin A tail domain interacting protein
  • Myosin essential light chain ELC
  • Myosin-A
KeywordsMOTOR PROTEIN / Myosin A / Myosin / Plasmodium / Myosin XIV / Myosin 14
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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Kinesin motor domain superfamily / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Calmodulin / Myosin-A / Myosin essential light chain ELC
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMoussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.B. / Robert-Paganin, J. / Trybus, K.M. / Houdusse, A.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI132378
CitationJournal: Elife / Year: 2020
Title: Full-length Plasmodium falciparum myosin A and essential light chain PfELC structures provide new anti-malarial targets.
Authors: Moussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.B. / Haase, S. / Blake, T.C.A. / Baum, J. / Robert-Paganin, J. / Trybus, K.M. / Houdusse, A.
History
DepositionMar 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)132,4809
Polymers131,6783
Non-polymers8026
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-118 kcal/mol
Surface area47930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.672, 114.685, 169.461
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 / PfM-A


Mass: 92474.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF13_0233 / 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 (isolate 3D7) (eukaryote)
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 (isolate 3D7) (eukaryote)
Gene: PF3D7_1017500 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IJM4

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Non-polymers , 5 types, 296 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.9M Ammonium sulfate, 0.1M Sodium HEPES pH 6.8, 2% PEG400

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Data collection

DiffractionMean temperature: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.906019 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906019 Å / Relative weight: 1
ReflectionResolution: 2.55→25.7 Å / Num. obs: 57507 / % possible obs: 99.62 % / Redundancy: 11.2 % / CC1/2: 0.998 / Net I/σ(I): 10.57
Reflection shellResolution: 2.55→2.641 Å / Num. unique obs: 5563 / CC1/2: 0.505

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I7D

6i7d


Resolution: 2.55→25.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2795 4.86 %RANDOM
Rwork0.195 ---
obs0.197 57507 99.8 %-
Displacement parametersBiso max: 188.77 Å2 / Biso mean: 79.51 Å2 / Biso min: 32.63 Å2
Baniso -1Baniso -2Baniso -3
1--11.991 Å20 Å20 Å2
2--8.8294 Å20 Å2
3---3.1616 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.55→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 47 290 8882
Biso mean--83.16 69.7 -
Num. residues----1070
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3175SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1232HARMONIC5
X-RAY DIFFRACTIONt_it8760HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1168SEMIHARMONIC5
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_contact10159SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8760HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11818HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 2.55→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 197 4.82 %
Rwork0.249 3889 -
all0.252 4086 -
obs--97.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3410.0065-0.10580.28360.26440.78910.04260.07080.0269-0.0333-0.05230.0333-0.0755-0.10810.0097-0.08860.01920.015-0.1820.0193-0.0955-3.4192-1.946829.0844
24.4246-1.0720.27671.2661-0.19870.7751-0.0010.32440.2328-0.181-0.0704-0.1728-0.09960.54420.0714-0.167-0.07970.04680.07030.0111-0.214235.926813.26253.764
32.78820.98250.10893.9829-0.73231.9559-0.0418-0.0945-0.30560.16380.1057-0.1520.11860.0016-0.0639-0.09880.0087-0.0304-0.125-0.0146-0.18539.10390.684473.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 818
2X-RAY DIFFRACTION2{ B|* }B28 - 158
3X-RAY DIFFRACTION3{ E|* }E2 - 134

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