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- PDB-6ycz: Plasmodium falciparum Myosin A delta-Nter, Post-Rigor state -

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Basic information

Entry
Database: PDB / ID: 6ycz
TitlePlasmodium falciparum Myosin A delta-Nter, Post-Rigor state
Components
  • Myosin A tail domain interacting protein
  • Myosin-A
  • Uncharacterized protein
KeywordsMOTOR PROTEIN / Myosin A / Myosin / Plasmodium / Myosin XIV / Myosin 14
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 / calcium ion binding / ATP binding / membrane / 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 / 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 / Myosin A tail domain interacting protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 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
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Plasmodium Myosin A motor properties are tuned by multiple sequence and structural adaptations
Authors: Moussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.M. / Robert-Paganin, J. / Houdusse, A.
History
DepositionMar 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: 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 tail domain interacting protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,46210
Polymers131,5983
Non-polymers8647
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-109 kcal/mol
Surface area47770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.080, 114.430, 170.710
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 ABC

#1: Protein Myosin-A / PfM-A


Mass: 92394.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / 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 NF54) (eukaryote)
Strain: isolate NF54 / Gene: CK202_1873, PFNF54_03975 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K1J7
#3: Protein Uncharacterized protein


Mass: 15692.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Gene: CK202_4702 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BQX1

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Non-polymers , 5 types, 11 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.0M Ammonium sulfate, 0.1M Sodium HEPES pH 7.5, 6% 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: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.27→48.3 Å / Num. obs: 27977 / % possible obs: 99.88 % / Redundancy: 12.8 % / CC1/2: 0.992 / Net I/σ(I): 9.02
Reflection shellResolution: 3.27→3.387 Å / Num. unique obs: 2748 / CC1/2: 0.553

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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: 3.27→48.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.884 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.4
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1399 5 %RANDOM
Rwork0.179 ---
obs0.182 27975 100 %-
Displacement parametersBiso max: 196.83 Å2 / Biso mean: 92.68 Å2 / Biso min: 32.25 Å2
Baniso -1Baniso -2Baniso -3
1--20.0053 Å20 Å20 Å2
2--11.5063 Å20 Å2
3---8.499 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 3.27→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8438 0 63 4 8505
Biso mean--80.76 63.85 -
Num. residues----1057
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3157SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1230HARMONIC5
X-RAY DIFFRACTIONt_it8715HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1156SEMIHARMONIC5
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_contact10182SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8715HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11780HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion22.86
LS refinement shellResolution: 3.27→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.294 145 5 %
Rwork0.221 2753 -
all0.225 2898 -
obs--99.86 %
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)
10.32270.015-0.06830.24510.19090.86210.0150.07330.0416-0.0191-0.04030.027-0.0754-0.11080.02530.04290.01510.0206-0.14870.0191-0.0847-3.4255-2.269629.0293
24.2152-1.1384-0.43041.2891-0.22991.3906-0.02120.35720.2426-0.2736-0.1606-0.0226-0.07330.54420.18170.0244-0.10650.07270.12950.0342-0.293936.507312.824254.1027
33.1050.54180.12074.7469-0.7162.2812-0.0772-0.085-0.25130.19170.1852-0.03870.07950.0303-0.1079-0.00930.0168-0.0427-0.1078-0.015-0.21039.73210.492474.4706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 1101
2X-RAY DIFFRACTION2{ B|* }B74 - 204
3X-RAY DIFFRACTION3{ C|* }C2 - 134

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