+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13864 | |||||||||
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Title | Leishmania major actin filament in ADP-state | |||||||||
Map data | Autosharpened and real-space symmetrized map from postprocess | |||||||||
Sample |
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Function / homology | Function and homology information kinetoplast / endonuclease activity / cytoskeleton / chromatin remodeling Similarity search - Function | |||||||||
Biological species | Leishmania major (eukaryote) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Kotila T / Muniyandi S / Lappalainen P / Huiskonen JT | |||||||||
Funding support | Finland, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13864.map.gz | 74.4 MB | EMDB map data format | |
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Header (meta data) | emd-13864-v30.xml emd-13864.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13864_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_13864.png | 108.3 KB | ||
Masks | emd_13864_msk_1.map | 91.1 MB | Mask map | |
Others | emd_13864_additional_1.map.gz emd_13864_half_map_1.map.gz emd_13864_half_map_2.map.gz | 84.9 MB 71.1 MB 71.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13864 | HTTPS FTP |
-Related structure data
Related structure data | 7q8cMC 7q8bC 7q8sC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13864.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Autosharpened and real-space symmetrized map from postprocess | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8617 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13864_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_13864_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map2
File | emd_13864_half_map_1.map | ||||||||||||
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Annotation | Half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map1
File | emd_13864_half_map_2.map | ||||||||||||
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Annotation | Half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bare, undecorated, ADP-state actin filament from the sample mixed...
Entire | Name: Bare, undecorated, ADP-state actin filament from the sample mixed with Leishmania major cofilin. |
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Components |
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-Supramolecule #1: Bare, undecorated, ADP-state actin filament from the sample mixed...
Supramolecule | Name: Bare, undecorated, ADP-state actin filament from the sample mixed with Leishmania major cofilin. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Leishmania major (eukaryote) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Actin
Macromolecule | Name: Actin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Leishmania major (eukaryote) |
Molecular weight | Theoretical: 42.063867 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 360 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | 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 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV Details: blot for 5 seconds before plunging, blot force 15. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 50 / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |