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- PDB-6tj6: T. gondii myosin A trimeric complex with ELC1, calcium-free -

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Basic information

Entry
Database: PDB / ID: 6tj6
TitleT. gondii myosin A trimeric complex with ELC1, calcium-free
Components
  • Calmodulin, putative
  • Myosin A
  • Myosin light chain TgMLC1
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 / cytoskeletal motor activity / actin filament organization / actin filament binding / actin binding ...mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity / actin filament organization / actin filament binding / actin 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
IMIDAZOLE / Calmodulin, putative / Myosin-A / Myosin light chain MLC1 / Myosin A
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)37,4904
Polymers37,4213
Non-polymers691
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS data agree with the crystal structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-39 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.831, 86.831, 54.938
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

#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: pET28A+(-)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
#3: Protein/peptide Myosin A


Mass: 5340.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_235470 / Plasmid: pET_GB-1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: S8G527, UniProt: O00934*PLUS
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000, Tris, Lithium Chloride

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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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→40.9 Å / Num. obs: 27763 / % possible obs: 99.91 % / Redundancy: 13.5 % / Biso Wilson estimate: 48.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.15 / Net I/σ(I): 31
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2711 / CC1/2: 0.72 / Rpim(I) all: 0.39 / Rrim(I) all: 1.41 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vt9

5vt9


Resolution: 2→40.9 Å / SU ML: 0.2589 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3194
RfactorNum. reflection% reflection
Rfree0.2248 1407 5.07 %
Rwork0.1896 --
obs0.1913 27759 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.41 Å2
Refinement stepCycle: LAST / Resolution: 2→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 5 147 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262515
X-RAY DIFFRACTIONf_angle_d0.59463394
X-RAY DIFFRACTIONf_chiral_restr0.0408366
X-RAY DIFFRACTIONf_plane_restr0.0036444
X-RAY DIFFRACTIONf_dihedral_angle_d16.14911531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.34561290.29892584X-RAY DIFFRACTION99.38
2.07-2.160.29641540.26022618X-RAY DIFFRACTION100
2.16-2.250.32441440.24992612X-RAY DIFFRACTION99.96
2.25-2.370.28331430.24162635X-RAY DIFFRACTION100
2.37-2.520.25291650.2252595X-RAY DIFFRACTION99.96
2.52-2.720.25631470.21432628X-RAY DIFFRACTION100
2.72-2.990.27191400.22382628X-RAY DIFFRACTION100
2.99-3.420.23221070.21852675X-RAY DIFFRACTION100
3.42-4.310.19271580.16742635X-RAY DIFFRACTION100
4.31-43.320.18821200.15182742X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -14.3905764905 Å / Origin y: -43.6774644172 Å / Origin z: -11.0030210361 Å
111213212223313233
T0.379179466173 Å2-0.00834391947538 Å20.0574934924796 Å2-0.448966788645 Å20.073588957889 Å2--0.426671493232 Å2
L1.94369873249 °2-0.935628002539 °2-0.780969816366 °2-1.44076132312 °21.42961511985 °2--1.3615390233 °2
S-0.160464603382 Å °-0.00859519213231 Å °0.00696212041907 Å °-0.0219414411507 Å °0.224471979815 Å °-0.171292374749 Å °-0.0173991800462 Å °0.293403545489 Å °-0.0499996107637 Å °
Refinement TLS groupSelection details: all

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