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- PDB-6i7d: Plasmodium falciparum Myosin A, post-rigor and rigor-like states -

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Basic information

Entry
Database: PDB / ID: 6i7d
TitlePlasmodium falciparum Myosin A, post-rigor and rigor-like states
ComponentsMyosin-A
KeywordsMOTOR PROTEIN / Myosin A / Plasmodium falciparum / tunable mechanism
Function / homology
Function and homology information


pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsRobert-Paganin, J. / Auguin, D. / Moussaoui, D. / Jousset, G. / Baum, J. / Trybus, K.M. / Houdusse, A.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
Human Frontier Science ProgramRGY0066/2016 United States
Wellcome Trust109007/Z/15/A United Kingdom
Wellcome Trust100993/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Plasmodium myosin A drives parasite invasion by an atypical force generating mechanism.
Authors: Robert-Paganin, J. / Robblee, J.P. / Auguin, D. / Blake, T.C.A. / Bookwalter, C.S. / Krementsova, E.B. / Moussaoui, D. / Previs, M.J. / Jousset, G. / Baum, J. / Trybus, K.M. / Houdusse, A.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Myosin-A
D: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,4937
Polymers346,2774
Non-polymers2163
Water7,620423
1
A: Myosin-A


Theoretical massNumber of molelcules
Total (without water)86,5691
Polymers86,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6312
Polymers86,5691
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myosin-A


Theoretical massNumber of molelcules
Total (without water)86,5691
Polymers86,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7233
Polymers86,5691
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.520, 258.730, 103.090
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Myosin-A / PfM-A


Mass: 86569.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF13_0233 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDR3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 18 % PEG 3350; 100 mM glycine

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.906019 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906019 Å / Relative weight: 1
ReflectionResolution: 2.82→49.19 Å / Num. obs: 78760 / % possible obs: 98.75 % / Redundancy: 5.1 % / Biso Wilson estimate: 89.3 Å2 / Net I/σ(I): 12.54
Reflection shellResolution: 2.82→2.921 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OS8

2os8


Resolution: 2.82→49.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.365
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3938 5 %RANDOM
Rwork0.187 ---
obs0.19 78760 98.8 %-
Displacement parametersBiso mean: 71.53 Å2
Baniso -1Baniso -2Baniso -3
1--5.8349 Å20 Å2-1.6206 Å2
2--9.2837 Å20 Å2
3----3.4487 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.82→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23850 0 54 423 24327
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0124352HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2232872HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8731SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes684HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3436HARMONIC5
X-RAY DIFFRACTIONt_it24352HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion21.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3252SEMIHARMONIC5
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_contact27691SEMIHARMONIC4
LS refinement shellResolution: 2.82→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 282 4.98 %
Rwork0.24 5375 -
all0.244 5657 -
obs--95.73 %

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