+Open data
-Basic information
Entry | Database: PDB / ID: 7q8c | |||||||||
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Title | Leishmania major actin filament in ADP-state | |||||||||
Components | Actin | |||||||||
Keywords | STRUCTURAL PROTEIN / Actin / Filament / Parasite / ADP-Pi | |||||||||
Function / homology | Function and homology information kinetoplast / endonuclease activity / cytoskeleton / chromatin remodeling Similarity search - Function | |||||||||
Biological species | Leishmania major (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Kotila, T. / Muniyandi, S. / Lappalainen, P. / Huiskonen, J.T. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q8c.cif.gz | 325.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q8c.ent.gz | 272 KB | Display | PDB format |
PDBx/mmJSON format | 7q8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q8c ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q8c | HTTPS FTP |
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-Related structure data
Related structure data | 13864MC 7q8bC 7q8sC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42063.867 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACT, LMJF_04_1230 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U1E8 #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Bare, undecorated, ADP-state actin filament from the sample mixed with Leishmania major cofilin. Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Leishmania major (eukaryote) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 Details: 10 mM HEPES, 125 mM NaCl, 5 mM KCl, 0.2 mM ATP, 0.4 mM EGTA, 1 mM MgCl2, 1 mM DTT |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279.15 K / Details: blot for 5 seconds before plunging, blot force 15 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 50 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -166.54 ° / Axial rise/subunit: 28.4 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232527 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6DJO Pdb chain-ID: A |