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Yorodumi- EMDB-15104: Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- nucleotide state. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15104 | |||||||||||||||
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Title | Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- nucleotide state. | |||||||||||||||
Map data | Sharpened, local-resolution filtered cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state. | |||||||||||||||
Sample |
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Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / rabbit (rabbit) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.17 Å | |||||||||||||||
Authors | Oosterheert W / Klink BU / Belyy A / Pospich S / Raunser S | |||||||||||||||
Funding support | European Union, Germany, 4 items
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Citation | Journal: Nature / Year: 2022 Title: Structural basis of actin filament assembly and aging. Authors: Wout Oosterheert / Björn U Klink / Alexander Belyy / Sabrina Pospich / Stefan Raunser / Abstract: The dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state. It remains unclear how F-actin hydrolyses ATP and ...The dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state. It remains unclear how F-actin hydrolyses ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here we present cryo-electron microscopy structures of F-actin in all nucleotide states, polymerized in the presence of Mg or Ca at approximately 2.2 Å resolution. The structures show that actin polymerization induces the relocation of water molecules in the nucleotide-binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (P) is closed in all structures, indicating that P release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and P release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of water molecules in the nucleotide-binding pocket explain why Ca-actin shows slower polymerization rates than Mg-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15104.map.gz | 129.5 MB | EMDB map data format | |
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Header (meta data) | emd-15104-v30.xml emd-15104.xml | 41.6 KB 41.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15104_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_15104.png | 89.8 KB | ||
Masks | emd_15104_msk_1.map emd_15104_msk_2.map | 216 MB 216 MB | Mask map | |
Others | emd_15104_additional_1.map.gz emd_15104_additional_2.map.gz emd_15104_additional_3.map.gz emd_15104_additional_4.map.gz emd_15104_additional_5.map.gz emd_15104_additional_6.map.gz emd_15104_additional_7.map.gz emd_15104_additional_8.map.gz emd_15104_additional_9.map.gz emd_15104_half_map_1.map.gz emd_15104_half_map_2.map.gz | 168.3 MB 129.7 MB 168.8 MB 171 MB 170.9 MB 130.1 MB 169.2 MB 170.9 MB 170.9 MB 170.6 MB 170.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15104 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15104 | HTTPS FTP |
-Validation report
Summary document | emd_15104_validation.pdf.gz | 671.4 KB | Display | EMDB validaton report |
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Full document | emd_15104_full_validation.pdf.gz | 670.9 KB | Display | |
Data in XML | emd_15104_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_15104_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15104 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15104 | HTTPS FTP |
-Related structure data
Related structure data | 8a2rMC 8a2sC 8a2tC 8a2uC 8a2yC 8a2zC M: atomic model generated by this map C: citing same article (ref.) |
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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_15104.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened, local-resolution filtered cryo-EM density map of F-actin in the ADP-BeF3- nucleotide state. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.695 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Mask #2
+Additional map: 3D-refined, unsharpened cryo-EM density map of F-actin in...
+Additional map: Sharpened, local-resolution filtered cryo-EM density map of F-actin...
+Additional map: 3D-refined, unsharpened cryo-EM density map of F-actin in...
+Additional map: Unfiltered half map 1 of F-actin in the...
+Additional map: Unfiltered half map 2 of F-actin in the...
+Additional map: Sharpened, local-resolution filtered cryo-EM density map of F-actin...
+Additional map: 3D-refined, unsharpened cryo-EM density map of F-actin in...
+Additional map: Unfiltered half map 1 of F-actin in the...
+Additional map: Unfiltered half map 2 of F-actin in the...
+Half map: Unfiltered half map 1 of F-actin in the ADP-BeF3- nucleotide state.
+Half map: Unfiltered half map 2 of F-actin in the ADP-BeF3- nucleotide state.
-Sample components
-Entire : rabbit skeletal alpha-actin in the filamentous state.
Entire | Name: rabbit skeletal alpha-actin in the filamentous state. |
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Components |
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-Supramolecule #1: rabbit skeletal alpha-actin in the filamentous state.
Supramolecule | Name: rabbit skeletal alpha-actin in the filamentous state. / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The helical rise of F-actin is 27.5 Angstrom, with a helical twist of ~166.5 degrees. |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 15.2 kDa/nm |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: rabbit (rabbit) / Tissue: skeletal muscle. |
Molecular weight | Theoretical: 41.875633 KDa |
Sequence | String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF |
-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: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 480 / 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 | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.13 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: F-buffer: 5 mM Tris pH 7.5, 100 mM KCl, 2 mM MgCl2, 2 mM NaN3, 1 mM DTT, 0.75 mM BeF2, 5 mM NaF. | ||||||||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV Details: The Vitrobot was operated at 13 degrees celsius and the samples were blotted for 9 seconds with a blot force of -25.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 15 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10822 / Average exposure time: 3.0 sec. / Average electron dose: 78.9 e/Å2 / Details: Images were collected in supperresolution mode. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |