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- PDB-6tj5: T. gondii myosin A trimeric complex with ELC1 -

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Basic information

Entry
Database: PDB / ID: 6tj5
TitleT. gondii myosin A trimeric complex with ELC1
Components
  • Calmodulin, putative
  • Myosin light chain TgMLC1
  • Myosin-A
KeywordsMOTOR PROTEIN / motility / glideosome / light chain / myosin
Function / homology
Function and homology information


mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding / vesicle / calcium ion binding ...mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand domain pair ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin, putative / Myosin-A / Myosin light chain MLC1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsPazicky, S. / Loew, C.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
Joachim Herz Foundation800026 Germany
Swedish Research Council621-2013-5905 Sweden
CitationJournal: Commun Biol / Year: 2020
Title: Structural role of essential light chains in the apicomplexan glideosome.
Authors: Pazicky, S. / Dhamotharan, K. / Kaszuba, K. / Mertens, H.D.T. / Gilberger, T. / Svergun, D. / Kosinski, J. / Weininger, U. / Low, C.
History
DepositionNov 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Calmodulin, putative
B: Myosin light chain TgMLC1
C: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4975
Polymers37,4213
Non-polymers762
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS measurements show that the complex agrees with the crystal structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-58 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.317, 87.317, 56.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Calmodulin, putative


Mass: 14881.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: BN1205_016670 / Plasmid: pET28(+)-TEV / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0F7UZ05
#2: Protein Myosin light chain TgMLC1


Mass: 17198.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pNIC_CTHF / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q95UJ7

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Myosin-A / MyoA / TgM-A


Mass: 5340.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pET_GB-1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00934

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Non-polymers , 3 types, 66 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Ethylene Glycol, PEG 8000, Tris, Bicin, Sodium Nitrate, Sodium Phosphate dibasic, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.394→47.58 Å / Num. obs: 17027 / % possible obs: 99.89 % / Redundancy: 13.3 % / Biso Wilson estimate: 58.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.03 / Rrim(I) all: 0.11 / Net I/σ(I): 19.06
Reflection shellResolution: 2.394→2.48 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.599 / Num. unique obs: 1718 / CC1/2: 0.718 / Rpim(I) all: 0.445 / Rrim(I) all: 1.66 / % possible all: 99.65

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tgh

3tgh


Resolution: 2.394→47.58 Å / SU ML: 0.2924 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.5924
RfactorNum. reflection% reflection
Rfree0.2312 828 4.87 %
Rwork0.1894 --
obs0.1915 17016 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.19 Å2
Refinement stepCycle: LAST / Resolution: 2.394→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 2 64 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842506
X-RAY DIFFRACTIONf_angle_d0.96963376
X-RAY DIFFRACTIONf_chiral_restr0.0544363
X-RAY DIFFRACTIONf_plane_restr0.0058440
X-RAY DIFFRACTIONf_dihedral_angle_d3.08341525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.394-2.540.331340.28162658X-RAY DIFFRACTION99.68
2.54-2.740.32261310.25662698X-RAY DIFFRACTION99.89
2.74-3.020.31871240.23632700X-RAY DIFFRACTION99.93
3.02-3.450.29321460.22582659X-RAY DIFFRACTION100
3.45-4.350.20411230.16882745X-RAY DIFFRACTION100
4.35-47.580.18931700.15772728X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 14.1704529334 Å / Origin y: 43.7500027671 Å / Origin z: 35.2275054663 Å
111213212223313233
T0.342888075994 Å20.0409809835373 Å2-0.0164432987391 Å2-0.476899390576 Å2-0.0922717914488 Å2--0.454513769679 Å2
L2.61696872903 °2-0.795403532861 °21.40045905227 °2-1.59286482692 °2-1.85340335218 °2--2.37213031428 °2
S-0.249688910981 Å °-0.078317715247 Å °0.0503865114449 Å °-0.0111546982153 Å °0.333039885211 Å °0.227923277767 Å °-0.0423487814992 Å °-0.504693651872 Å °-0.0515268241015 Å °
Refinement TLS groupSelection details: all

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