+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27565 | |||||||||
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Title | Cryo-EM structure of nonmuscle gamma-actin | |||||||||
Map data | Cryo-EM structure of nonmuscle gamma-actin | |||||||||
Sample |
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Function / homology | Function and homology information basal body patch / tight junction assembly / regulation of transepithelial transport / morphogenesis of a polarized epithelium / profilin binding / protein localization to bicellular tight junction / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / dense body / Gap junction degradation ...basal body patch / tight junction assembly / regulation of transepithelial transport / morphogenesis of a polarized epithelium / profilin binding / protein localization to bicellular tight junction / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / regulation of stress fiber assembly / Adherens junctions interactions / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / sarcomere organization / positive regulation of wound healing / myofibril / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / filamentous actin / Recycling pathway of L1 / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / axonogenesis / platelet aggregation / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Schaffer collateral - CA1 synapse / cellular response to type II interferon / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / Clathrin-mediated endocytosis / angiogenesis / blood microparticle / cytoskeleton / hydrolase activity / positive regulation of cell migration / axon / focal adhesion / ubiquitin protein ligase binding / synapse / positive regulation of gene expression / protein kinase binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||
Authors | Arora AS / Huang HL / Heissler SM / Chinthalapudi K | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27565.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-27565-v30.xml emd-27565.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27565_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_27565.png | 90.5 KB | ||
Others | emd_27565_half_map_1.map.gz emd_27565_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27565 | HTTPS FTP |
-Validation report
Summary document | emd_27565_validation.pdf.gz | 997.4 KB | Display | EMDB validaton report |
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Full document | emd_27565_full_validation.pdf.gz | 997 KB | Display | |
Data in XML | emd_27565_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_27565_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27565 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27565 | HTTPS FTP |
-Related structure data
Related structure data | 8dnfMC 8dmxC 8dmyC 8dnhC 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_27565.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of nonmuscle gamma-actin | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.891 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of nonmuscle gamma-actin
File | emd_27565_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of nonmuscle gamma-actin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of nonmuscle gamma-actin
File | emd_27565_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of nonmuscle gamma-actin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : actin
Entire | Name: actin |
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Components |
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-Supramolecule #1: actin
Supramolecule | Name: actin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Actin, cytoplasmic 2, N-terminally processed
Macromolecule | Name: Actin, cytoplasmic 2, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.746625 KDa |
Recombinant expression | Organism: Pichia (fungus) |
Sequence | String: (ACE)EEEIAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE (HIC)GIVTNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRT TGIVMDSGDG ...String: (ACE)EEEIAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE (HIC)GIVTNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRT TGIVMDSGDG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLE KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP G IADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: C-flat / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs-corrected microscope / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2952 / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |