+Open data
-Basic information
Entry | Database: PDB / ID: 8dnh | ||||||
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Title | Cryo-EM structure of nonmuscle beta-actin | ||||||
Components | Actin, cytoplasmic 1, N-terminally processed | ||||||
Keywords | STRUCTURAL PROTEIN / cytoskeleton | ||||||
Function / homology | Function and homology information positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / protein localization to adherens junction / nBAF complex / postsynaptic actin cytoskeleton ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / protein localization to adherens junction / nBAF complex / postsynaptic actin cytoskeleton / brahma complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / RSC-type complex / Prefoldin mediated transfer of substrate to CCT/TriC / RHOF GTPase cycle / Adherens junctions interactions / tight junction / regulation of mitotic metaphase/anaphase transition / 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 / SWI/SNF complex / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / negative regulation of cell differentiation / calyx of Held / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / substantia nigra development / EPHB-mediated forward signaling / axonogenesis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / platelet aggregation / negative regulation of protein binding / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / positive regulation of cell differentiation / RHO GTPases Activate Formins / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / 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 / DNA Damage Recognition in GG-NER / tau protein binding / B-WICH complex positively regulates rRNA expression / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / nuclear matrix / cytoplasmic ribonucleoprotein granule / 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 / UCH proteinases / cell-cell junction / nucleosome / actin cytoskeleton / lamellipodium / Clathrin-mediated endocytosis / presynapse / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 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 | 8dnh.cif.gz | 291.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dnh.ent.gz | 239 KB | Display | PDB format |
PDBx/mmJSON format | 8dnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dnh_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8dnh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8dnh_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 8dnh_validation.cif.gz | 75.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/8dnh ftp://data.pdbj.org/pub/pdb/validation_reports/dn/8dnh | HTTPS FTP |
-Related structure data
Related structure data | 27572MC 8dmxC 8dmyC 8dnfC 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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1 |
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-Components
#1: Protein | Mass: 41690.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Komagataella pastoris (fungus) / References: UniProt: P60709 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: filamentous actin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Pichia (fungus) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: filamentous beta actin with Mg. ADP |
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: 2000 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: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1352 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 263911 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263911 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | B value: 81 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6DJO | ||||||||||||||||||||||||||||||
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