+Open data
-Basic information
Entry | Database: PDB / ID: 8dmx | ||||||
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Title | Cryo-EM structure of skeletal muscle alpha-actin | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | STRUCTURAL PROTEIN / cytoskeleton | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Arora, A.S. / Huang, H.L. / Heissler, S.M. / Chinthalapudi, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2023 Title: Structural insights into actin isoforms. Authors: Amandeep S Arora / Hsiang-Ling Huang / Ramanpreet Singh / Yoshie Narui / Andrejus Suchenko / Tomoyuki Hatano / Sarah M Heissler / Mohan K Balasubramanian / Krishna Chinthalapudi / Abstract: Actin isoforms organize into distinct networks that are essential for the normal function of eukaryotic cells. Despite a high level of sequence and structure conservation, subtle differences in their ...Actin isoforms organize into distinct networks that are essential for the normal function of eukaryotic cells. Despite a high level of sequence and structure conservation, subtle differences in their design principles determine the interaction with myosin motors and actin-binding proteins. Therefore, identifying how the structure of actin isoforms relates to function is important for our understanding of normal cytoskeletal physiology. Here, we report the high-resolution structures of filamentous skeletal muscle α-actin (3.37 Å), cardiac muscle α-actin (3.07 Å), ß-actin (2.99 Å), and γ-actin (3.38 Å) in the Mg·ADP state with their native post-translational modifications. The structures revealed isoform-specific conformations of the N-terminus that shift closer to the filament surface upon myosin binding, thereby establishing isoform-specific interfaces. Collectively, the structures of single-isotype, post-translationally modified bare skeletal muscle α-actin, cardiac muscle α-actin, ß-actin, and γ-actin reveal general principles, similarities, and differences between isoforms. They complement the repertoire of known actin structures and allow for a comprehensive understanding of in vitro and in vivo functions of actin isoforms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dmx.cif.gz | 287.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dmx.ent.gz | 236.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dmx_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8dmx_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8dmx_validation.xml.gz | 58.3 KB | Display | |
Data in CIF | 8dmx_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/8dmx ftp://data.pdbj.org/pub/pdb/validation_reports/dm/8dmx | HTTPS FTP |
-Related structure data
Related structure data | 27548MC 8dmyC 8dnfC 8dnhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / Has ligand of interest | N | |
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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: actin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Organ: skeletal muscle |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: C-flat |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 200 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2046 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Spherical aberration corrector: Cs-corrected microscope |
-Processing
Software | Name: PHENIX / Version: 1.20rc3_4406: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -166 ° / Axial rise/subunit: 28 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||
Particle selection | Details: Single Particle | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261195 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||
Atomic model building | B value: 90 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6DJO Pdb chain-ID: A | ||||||||||||||||||||||||||||||
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