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- PDB-6ycx: Plasmodium falciparum Myosin A full-length, pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 6ycx
TitlePlasmodium falciparum Myosin A full-length, pre-powerstroke state
Components
  • (Uncharacterized ...) x 2
  • Myosin A tail domain interacting protein
  • Myosin-A
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 / VANADATE ION / 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: 3.99 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 1.1Jan 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
D: Myosin A tail domain interacting protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Myosin A tail domain interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,50312
Polymers263,3706
Non-polymers1,1336
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17680 Å2
ΔGint-155 kcal/mol
Surface area94190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.240, 287.430, 78.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABDH

#1: Protein Myosin-A / PfM-A


Mass: 92474.305 Da / Num. of mol.: 2
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.: 2
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

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Uncharacterized ... , 2 types, 2 molecules FG

#3: Protein Uncharacterized protein


Mass: 15706.822 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
#4: 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 , 3 types, 6 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: 1M Na Citrate tribasic; 0.01M Na Borate pH 8.0

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.99→48.4 Å / Num. obs: 33243 / % possible obs: 99.49 % / Redundancy: 10.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.4443 / Net I/σ(I): 4.19
Reflection shellResolution: 3.99→4.133 Å / Num. unique obs: 3194 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I7E

6i7e


Resolution: 3.99→48.4 Å / Cor.coef. Fo:Fc: 0.631 / Cor.coef. Fo:Fc free: 0.602 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.773
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1663 5 %RANDOM
Rwork0.237 ---
obs0.239 33243 99.6 %-
Displacement parametersBiso max: 293.96 Å2 / Biso mean: 70.59 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--24.1708 Å20 Å20 Å2
2--23.0956 Å20 Å2
3---1.0752 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: final / Resolution: 3.99→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17193 0 66 0 17259
Biso mean--23.55 --
Num. residues----2155
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6473SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes529HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2529HARMONIC5
X-RAY DIFFRACTIONt_it17797HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2375SEMIHARMONIC5
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_contact21154SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17797HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg24068HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion1.92
X-RAY DIFFRACTIONt_other_torsion22.81
LS refinement shellResolution: 3.99→4.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.258 138 5.02 %
Rwork0.242 2610 -
all0.243 2748 -
obs--95.83 %
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)
10.22730.18520.21861.26280.4621.38360.038-0.0906-0.08450.0345-0.00150.17310.0213-0.5442-0.0365-0.3040.0139-0.0211-0.03040.1394-0.30145.9629286.947-47.2117
20-0.1947-0.39450.75290.20891.58170.29940.13380.3376-0.5218-0.05480.4778-0.5442-0.5442-0.24470.3040.1520.1520.00460.1520.149555.9128342.061-66.8549
31.34182.9104-1.17298.31121.13247.3996-0.060.5442-0.3325-0.31510.17220.2560.1665-0.1098-0.11220.3039-0.152-0.1520.19910.12420.001734.5881246.258-105.349
46.7930.58492.7048.31060.99648.14690.0719-0.0238-0.1033-0.12790.1275-0.23080.07550.2277-0.19940.2251-0.152-0.1209-0.3010.0792-0.30457.4026263.628-83.4141
53.1221-0.9725-2.91047.8727-0.88213.99940.0355-0.0231-0.14880.1760.0749-0.18120.06540.3438-0.11040.3040.15190.1520.26130.1520.143874.0236359.674-29.8176
60-0.53441.99318.3117-2.90275.66190.0505-0.37930.2971-0.12860.0111-0.0285-0.00820.2796-0.06160.3040.1520.152-0.08320.04080.202955.1213384.575-11.9713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 1001
2X-RAY DIFFRACTION2{ B|* }B2 - 1001
3X-RAY DIFFRACTION3{ D|* }D72 - 204
4X-RAY DIFFRACTION4{ F|* }F2 - 134
5X-RAY DIFFRACTION5{ G|* }G3 - 134
6X-RAY DIFFRACTION6{ H|* }H72 - 204

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