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- EMDB-41583: Actin 1 from T. gondii in filaments bound to MgADP -

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Basic information

Entry
Database: EMDB / ID: EMD-41583
TitleActin 1 from T. gondii in filaments bound to MgADP
Map dataT. gondii Act1; Density Modified Map from Helical Reconstruction
Sample
  • Complex: Filament of Actin 1 from T. gondii with MgADP
    • Protein or peptide: Actin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water
KeywordsActin / cytoskeleton / toxoplasmosis / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesToxoplasma gondii (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHvorecny KL / Sladewski TE / Heaslip AT / Kollman JM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI145111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138316 United States
CitationJournal: Nat Commun / Year: 2024
Title: Toxoplasma gondii actin filaments are tuned for rapid disassembly and turnover.
Authors: Kelli L Hvorecny / Thomas E Sladewski / Enrique M De La Cruz / Justin M Kollman / Aoife T Heaslip /
Abstract: The cytoskeletal protein actin plays a critical role in the pathogenicity of the intracellular parasite, Toxoplasma gondii, mediating invasion and egress, cargo transport, and organelle inheritance. ...The cytoskeletal protein actin plays a critical role in the pathogenicity of the intracellular parasite, Toxoplasma gondii, mediating invasion and egress, cargo transport, and organelle inheritance. Advances in live cell imaging have revealed extensive filamentous actin networks in the Apicomplexan parasite, but there are conflicting data regarding the biochemical and biophysical properties of Toxoplasma actin. Here, we imaged the in vitro assembly of individual Toxoplasma actin filaments in real time, showing that native, unstabilized filaments grow tens of microns in length. Unlike skeletal muscle actin, Toxoplasma filaments intrinsically undergo rapid treadmilling due to a high critical concentration, fast monomer dissociation, and rapid nucleotide exchange. Cryo-EM structures of jasplakinolide-stabilized and native (i.e. unstabilized) filaments show an architecture like skeletal actin, with differences in assembly contacts in the D-loop that explain the dynamic nature of the filament, likely a conserved feature of Apicomplexan actin. This work demonstrates that evolutionary changes at assembly interfaces can tune the dynamic properties of actin filaments without disrupting their conserved structure.
History
DepositionAug 9, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41583.png

Downloads & links

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Map

FileDownload / File: emd_41583.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT. gondii Act1; Density Modified Map from Helical Reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 384 pix.
= 323.328 Å		0.84 Å/pix.
x 384 pix.
= 323.328 Å		0.84 Å/pix.
x 384 pix.
= 323.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25
Minimum - Maximum-8.379894 - 25.086136
Average (Standard dev.)0.000032911907 (±0.35868388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 323.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: T. gondii Act1; Half Map from Local Refinement (3 protomer)

Fileemd_41583_additional_1.map
AnnotationT. gondii Act1; Half Map from Local Refinement (3 protomer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: T. gondii Act1; Half Map from Local Refinement (3 protomer)

Fileemd_41583_additional_2.map
AnnotationT. gondii Act1; Half Map from Local Refinement (3 protomer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: T. gondii Act1; Density Modified Map from Local...

Fileemd_41583_additional_3.map
AnnotationT. gondii Act1; Density Modified Map from Local Refinement (3 protomer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T. gondii Act1; Half Map from Helical Reconstruction

Fileemd_41583_half_map_1.map
AnnotationT. gondii Act1; Half Map from Helical Reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T. gondii Act1; Half Map from Helical Reconstruction

Fileemd_41583_half_map_2.map
AnnotationT. gondii Act1; Half Map from Helical Reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament of Actin 1 from T. gondii with MgADP

EntireName: Filament of Actin 1 from T. gondii with MgADP
Components
  • Complex: Filament of Actin 1 from T. gondii with MgADP
    • Protein or peptide: Actin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Filament of Actin 1 from T. gondii with MgADP

SupramoleculeName: Filament of Actin 1 from T. gondii with MgADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Actin protomers from T. gondii assemble into a two-start helix
Source (natural)Organism: Toxoplasma gondii (eukaryote)

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Macromolecule #1: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Molecular weightTheoretical: 41.956711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADEEVQALV VDNGSGNVKA GVAGDDAPRA VFPSIVGKPK NPGIMVGMEE KDCYVGDEAQ SKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRVAP EEHPVLLTEA PLNPKANRER MTQIMFETFN VPAMYVAIQA VLSLYSSGRT TGIVLDSGDG V SHTVPIYE ...String:
MADEEVQALV VDNGSGNVKA GVAGDDAPRA VFPSIVGKPK NPGIMVGMEE KDCYVGDEAQ SKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRVAP EEHPVLLTEA PLNPKANRER MTQIMFETFN VPAMYVAIQA VLSLYSSGRT TGIVLDSGDG V SHTVPIYE GYALPHAIMR LDLAGRDLTE YMMKILHERG YGFTTSAEKE IVRDIKEKLC YIALDFDEEM KAAEDSSDIE KS YELPDGN IITVGNERFR CPEALFQPSF LGKEAAGVHR TTFDSIMKCD VDIRKDLYGN VVLSGGTTMY EGIGERLTKE LTS LAPSTM KIKVVAPPER KYSVWIGGSI LSSLSTFQQM WITKEEYDES GPSIVHRKCF

UniProtKB: Actin

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 30 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.6
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.85 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 28.1 Å
Applied symmetry - Helical parameters - Δ&Phi: -167 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PHENIX (ver. 1.20) / Number images used: 2248567
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8trm:
Actin 1 from T. gondii in filaments bound to MgADP

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