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- EMDB-13863: Leishmania major actin filament in ADP-Pi state -

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Basic information

Entry
Database: EMDB / ID: EMD-13863
TitleLeishmania major actin filament in ADP-Pi state
Map dataReal-space symmetrized and Phenix autosharpened map
Sample
  • Complex: Polymerized actin
    • Protein or peptide: Actin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
Function / homology
Function and homology information


kinetoplast / endonuclease activity / cytoskeleton / chromatin remodeling / ATP binding
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 speciesLeishmania major (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKotila T / Muniyandi S / Lappalainen P / Huiskonen JT
Funding support Finland, 2 items
OrganizationGrant numberCountry
Academy of Finland320161 Finland
Jane and Aatos Erkko Foundation4708679 Finland
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite.
Authors: Tommi Kotila / Hugo Wioland / Muniyandi Selvaraj / Konstantin Kogan / Lina Antenucci / Antoine Jégou / Juha T Huiskonen / Guillaume Romet-Lemonne / Pekka Lappalainen /
Abstract: Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, ...Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin 'cofactors', which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton.
History
DepositionNov 11, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13863.png

Downloads & links

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Map

FileDownload / File: emd_13863.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReal-space symmetrized and Phenix autosharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-10.067873 - 28.100874
Average (Standard dev.)-2.8628488e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 248.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13863_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocess from Relion

Fileemd_13863_additional_1.map
AnnotationPostprocess from Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_13863_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_13863_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polymerized actin

EntireName: Polymerized actin
Components
  • Complex: Polymerized actin
    • Protein or peptide: Actin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Polymerized actin

SupramoleculeName: Polymerized actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Leishmania major (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leishmania major (eukaryote)
Molecular weightTheoretical: 42.063867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADNEQSSIV CDNGSGMVKA GFSGDDAPRH VFPSIVGRPK NMQAMMGSAN KTVYVGDEAQ SKRGVLSLKY PIEHGIVTNW DDMEKIWHH TFYNELRVNP EQHNVLLTEA PMNPKQNREK MTQIMFETFN VPSLYIGIQA VLSLYSSGRT TGIVLDAGDG V THTVPIYE ...String:
MADNEQSSIV CDNGSGMVKA GFSGDDAPRH VFPSIVGRPK NMQAMMGSAN KTVYVGDEAQ SKRGVLSLKY PIEHGIVTNW DDMEKIWHH TFYNELRVNP EQHNVLLTEA PMNPKQNREK MTQIMFETFN VPSLYIGIQA VLSLYSSGRT TGIVLDAGDG V THTVPIYE GYSLPHAVRR VDMAGRDLTE YLMKIMMETG TTFTTTAEKE IVRNVKEQLC YVALDFEEEM TNSAKSANEE AF ELPDGNV MMVGNQRFRC PEVLFKPSLI GLDEAPGFPE MVYQSINKCD IDVRRELYGN IVLSGGSTMF LNLPERLAKE ISN LAPSSI KPKVVAPPER KYSVWIGGSI LSSLTTFQTM WVKKSEYDES GPSIVHNKCF

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 5 / 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: 5 / 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: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.2
Details: Phosphate buffered saline supplemented with 0.2 mM ATP, 1 mM MgCl2, 0.4 mM EGTA and 1 mM DTT.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 45 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.61 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 89543
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: INSILICO MODEL / In silico model: Initial model generated in Relion
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7q8b:
Leishmania major actin filament in ADP-Pi state

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