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Yorodumi- EMDB-24399: cryo-EM structure of the ADP state wild type myosin-15-F-actin complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24399 | ||||||||||||
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Title | cryo-EM structure of the ADP state wild type myosin-15-F-actin complex | ||||||||||||
Map data | cryo-EM structure of the ADP state wild type myosin-15-F-actin complex | ||||||||||||
Sample |
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Function / homology | Function and homology information actin-based cell projection / stereocilium bundle / Striated Muscle Contraction / stereocilium / myosin complex / inner ear morphogenesis / microfilament motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / response to light stimulus ...actin-based cell projection / stereocilium bundle / Striated Muscle Contraction / stereocilium / myosin complex / inner ear morphogenesis / microfilament motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / response to light stimulus / skeletal muscle fiber development / stress fiber / actin filament organization / actin filament / locomotory behavior / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) / Mus musculus (house mouse) / Chicken (chicken) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.63 Å | ||||||||||||
Authors | Gong R / 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_24399.map.gz | 284.7 MB | EMDB map data format | |
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Header (meta data) | emd-24399-v30.xml emd-24399.xml | 23.2 KB 23.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24399_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_24399.png | 166.4 KB | ||
Masks | emd_24399_msk_1.map | 512 MB | Mask map | |
Others | emd_24399_half_map_1.map.gz emd_24399_half_map_2.map.gz | 410.4 MB 410.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24399 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24399 | HTTPS FTP |
-Validation report
Summary document | emd_24399_validation.pdf.gz | 740 KB | Display | EMDB validaton report |
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Full document | emd_24399_full_validation.pdf.gz | 739.6 KB | Display | |
Data in XML | emd_24399_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | emd_24399_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24399 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24399 | HTTPS FTP |
-Related structure data
Related structure data | 7rb8MC 7r8vC 7r91C 7rb9C 7udtC 7uduC C: citing same article (ref.) M: atomic model generated by this map |
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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_24399.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 the ADP state wild type myosin-15-F-actin complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_24399_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half1
File | emd_24399_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_24399_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The ADP state wild type myosin15 in complex with filamentous actin
Entire | Name: The ADP state wild type myosin15 in complex with filamentous actin |
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Components |
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-Supramolecule #1: The ADP state wild type myosin15 in complex with filamentous actin
Supramolecule | Name: The ADP state wild type myosin15 in complex with filamentous actin type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Experimental: 5.4 kDa/nm |
-Supramolecule #2: Actin
Supramolecule | Name: Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallus (chicken) |
-Supramolecule #3: Isoform 3 of Unconventional myosin-XV
Supramolecule | Name: Isoform 3 of Unconventional myosin-XV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Chicken (chicken) |
Molecular weight | Theoretical: 41.63143 KDa |
Sequence | String: DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA ...String: DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA LPHAIMRLDL AGRDLTDYLM KILTERGYSF VTTAEREIVR DIKEKLCYVA LDFENEMATA ASSSSLEK S YELPDGQVIT IGNERFRCPE TLFQPSFIGM ESAGIHETTY NSIMKCDIDI RKDLYANNVM SGGTTMYPGI ADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF |
-Macromolecule #2: Isoform 3 of Unconventional myosin-XV
Macromolecule | Name: Isoform 3 of Unconventional myosin-XV / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 78.182703 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) |
Sequence | String: EDGVEDMTQL EDLQETTVLA NLKTRFERNL IYTYIGSILV SVNPYRMFAI YGPEQVQQYS GRALGENPPH LFAIANLAFA KMLDAKQNQ CVIISGESGS GKTEATKLIL RCLAAMNQRR DVMQQIKILE ATPLLEAFGN AKTVRNDNSS RFGKFVEIFL E GGVICGAI ...String: EDGVEDMTQL EDLQETTVLA NLKTRFERNL IYTYIGSILV SVNPYRMFAI YGPEQVQQYS GRALGENPPH LFAIANLAFA KMLDAKQNQ CVIISGESGS GKTEATKLIL RCLAAMNQRR DVMQQIKILE ATPLLEAFGN AKTVRNDNSS RFGKFVEIFL E GGVICGAI TSQYLLEKSR IVFQAKNERN YHIFYELLAG LPAQLRQAFS LQEAETYYYL NQGGNCEIAG KSDADDFRRL LA AMEVLGF TSEDQDSIFR ILASILHLGN VYFEKHETDA QEVASVVSAR EIQAVAELLQ VSPEGLQKAI TFKVTETIRE KIF TPLTVE SAVDARDAIA KVLYALLFGW LITRVNALVS PKQDTLSIAI LDIYGFEDLS FNSFEQLCIN YANENLQYLF NKIV FQEEQ EEYIREQMDW REIAFADNQP CINLISLKPY GILRILDDQC CFPQATDHTF LQKCHYHHGA NPLYSKPKMP LPEFT IKHY AGKVTYQVHK FLDKNHDQVR QDVLDLFVHS RTRVVAHLFS SHAAQTAPPR LGKSSSITRL YKAHTVAAKF QQSLLD LVE KMERCNPLFV RCLKPNHKKE PGLFEPDVMM AQLRYSGVLE TVRIRKEGFP VRLPFQVFID RYRCLVALKL NVPADGD MC VSLLSRLCTV TPDMYRVGIS KLFLKEHLHQ LLESMRERVQ NRA |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / 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 / Instrument: LEICA EM GP |
-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 / Number grids imaged: 1 / 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 / 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 |