+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24321 | ||||||||||||
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Title | Cryo-EM structure of the ADP state actin filament | ||||||||||||
Map data | Cryo-EM structure of F actin in the ADP state | ||||||||||||
Sample |
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Function / homology | Function and homology information Striated Muscle Contraction / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) / Chicken (chicken) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.82 Å | ||||||||||||
Authors | Gong R / Espinosa de los Reyes S / Reynolds MJ / Gurel P / Alushin GM | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia. Authors: Rui Gong / Fangfang Jiang / Zane G Moreland / Matthew J Reynolds / Santiago Espinosa de Los Reyes / Pinar Gurel / Arik Shams / James B Heidings / Michael R Bowl / Jonathan E Bird / Gregory M Alushin / Abstract: The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin ...The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin regulatory machinery to stereocilia tips, myosin-15 directly nucleates actin filament ("F-actin") assembly, which is disrupted by a progressive hearing loss mutation (p.D1647G, ""). Here, we present cryo-electron microscopy structures of myosin-15 bound to F-actin, providing a framework for interpreting the impacts of deafness mutations on motor activity and actin nucleation. Rigor myosin-15 evokes conformational changes in F-actin yet maintains flexibility in actin's D-loop, which mediates inter-subunit contacts, while the mutant locks the D-loop in a single conformation. Adenosine diphosphate-bound myosin-15 also locks the D-loop, which correspondingly blunts actin-polymerization stimulation. We propose myosin-15 enhances polymerization by bridging actin protomers, regulating nucleation efficiency by modulating actin's structural plasticity in a myosin nucleotide state-dependent manner. This tunable regulation of actin polymerization could be harnessed to precisely control stereocilium height. #1: Journal: Biorxiv / Year: 2021 Title: Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia Authors: Gong R / Jiang F / Moreland ZG / Reynolds MJ / Gurel PS / Shams A / Bowl MR / Bird JE / Alushin GM | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24321.map.gz | 287.3 MB | EMDB map data format | |
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Header (meta data) | emd-24321-v30.xml emd-24321.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24321_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_24321.png | 54.9 KB | ||
Masks | emd_24321_msk_1.map | 512 MB | Mask map | |
Others | emd_24321_half_map_1.map.gz emd_24321_half_map_2.map.gz | 410.7 MB 410.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24321 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24321 | HTTPS FTP |
-Validation report
Summary document | emd_24321_validation.pdf.gz | 660.3 KB | Display | EMDB validaton report |
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Full document | emd_24321_full_validation.pdf.gz | 659.9 KB | Display | |
Data in XML | emd_24321_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | emd_24321_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24321 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24321 | HTTPS FTP |
-Related structure data
Related structure data | 7r8vMC 7r91C 7rb8C 7rb9C 7udtC 7uduC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24321.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of F actin in the ADP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_24321_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: cryo-EM structure of F actin in the ADP state
File | emd_24321_half_map_1.map | ||||||||||||
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Annotation | cryo-EM structure of F actin in the ADP state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM structure of F actin in the ADP state
File | emd_24321_half_map_2.map | ||||||||||||
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Annotation | cryo-EM structure of F actin in the ADP state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : filamentous chicken skeletal muscle actin
Entire | Name: filamentous chicken skeletal muscle actin |
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Components |
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-Supramolecule #1: filamentous chicken skeletal muscle actin
Supramolecule | Name: filamentous chicken skeletal muscle actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: chicken skeletal muscle actin purified from fresh chicken breast |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 5.4 kDa/nm |
-Macromolecule #1: Actin, alpha skeletal muscle, intermediate form
Macromolecule | Name: Actin, alpha skeletal muscle, intermediate form / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Chicken (chicken) |
Molecular weight | Theoretical: 41.387227 KDa |
Sequence | String: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF |
-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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 Details: 10 mM imidazole pH 7.0, 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.01% NaN3 |
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K |
Details | chicken cytoskeletal actin purified from chicken breast muscle |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |