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- PDB-6zn3: Plasmodium facliparum glideosome trimeric sub-complex -

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Basic information

Entry
Database: PDB / ID: 6zn3
TitlePlasmodium facliparum glideosome trimeric sub-complex
Components
  • Myosin A tail domain interacting protein
  • Myosin essential light chain ELC
  • Myosin-A
KeywordsMOTOR PROTEIN / motility / glideosome / myosin / essential light chain
Function / homology
Function and homology information


pellicle / inner membrane pellicle complex / glideosome / myosin complex / myosin II complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin complex / myosin II complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Kinesin motor domain superfamily / : ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / 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
Calmodulin / Myosin-A / Myosin essential light chain ELC
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsPazicky, S. / Loew, C.
Funding support Sweden, Germany, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2013-5905 Sweden
Joachim Herz Stiftung800026 Germany
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
DepositionJul 6, 2020Deposition 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 31, 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

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Assembly

Deposited unit
A: Myosin essential light chain ELC
B: Myosin A tail domain interacting protein
C: Myosin-A
D: Myosin essential light chain ELC
E: Myosin A tail domain interacting protein
F: Myosin-A
G: Myosin essential light chain ELC
H: Myosin A tail domain interacting protein
I: Myosin-A
J: Myosin essential light chain ELC
K: Myosin A tail domain interacting protein
L: Myosin-A
M: Myosin essential light chain ELC
N: Myosin A tail domain interacting protein
O: Myosin-A


Theoretical massNumber of molelcules
Total (without water)188,04815
Polymers188,04815
Non-polymers00
Water543
1
A: Myosin essential light chain ELC
B: Myosin A tail domain interacting protein
C: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-44 kcal/mol
Surface area16350 Å2
MethodPISA
2
D: Myosin essential light chain ELC
E: Myosin A tail domain interacting protein
F: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area16440 Å2
MethodPISA
3
G: Myosin essential light chain ELC
H: Myosin A tail domain interacting protein
I: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-47 kcal/mol
Surface area16210 Å2
MethodPISA
4
J: Myosin essential light chain ELC
K: Myosin A tail domain interacting protein
L: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area16800 Å2
MethodPISA
5
M: Myosin essential light chain ELC
N: Myosin A tail domain interacting protein
O: Myosin-A


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,6103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-47 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.880, 211.880, 75.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Myosin essential light chain ELC


Mass: 15779.875 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1017500 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IJM4
#2: Protein
Myosin A tail domain interacting protein


Mass: 16788.572 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1246400 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8I4W8
#3: Protein/peptide
Myosin-A / PfM-A


Mass: 5041.055 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF13_0233 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IDR3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, ethylene glycol, di-ethyleneglycol, tri-ethyleneglycol, tetra-ethyleneglycol, penta-ethyleneglycol, imidazole, MES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.51→47.42 Å / Num. obs: 114354 / % possible obs: 83.53 % / Redundancy: 6.7 % / Biso Wilson estimate: 81.46 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0874 / Rpim(I) all: 0.03701 / Rrim(I) all: 0.09505 / Net I/σ(I): 12.69
Reflection shellResolution: 2.51→2.604 Å / Redundancy: 6.6 % / Rmerge(I) obs: 3.79 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 911 / CC1/2: 0.111 / CC star: 0.448 / Rpim(I) all: 1.602 / Rrim(I) all: 4.118 / % possible all: 7.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.17.1.3660refinement
STARANISOdata scaling
PHASER1.17.1.3660phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jt4, 4aom

6jt4

4aom


Resolution: 2.51→47.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.812 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 2.51 / ESU R: 0.314 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23756 4756 5 %RANDOM
Rwork0.20027 ---
obs0.20216 90855 83.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 2.51→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12965 0 0 3 12968
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.009 / Dev ideal target: 0.013 / Number: 13175
LS refinement shellResolution: 2.514→2.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 19 -
Rwork0.373 341 -
obs--4.27 %

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