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Yorodumi- PDB-9fjm: Cryo-EM structure of the phalloidin-bound pointed end of the acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fjm | ||||||||||||
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Title | Cryo-EM structure of the phalloidin-bound pointed end of the actin filament. | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / actin / phalloidin / filament / pointed end | ||||||||||||
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 / postsynaptic actin cytoskeleton / nBAF complex / protein localization to adherens junction ...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 / postsynaptic actin cytoskeleton / nBAF complex / protein localization to adherens junction / 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 / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / 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 / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / 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 / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / substantia nigra development / EPHB-mediated forward signaling / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / axonogenesis / platelet aggregation / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / 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 / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / 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 / UCH proteinases / Signaling by BRAF and RAF1 fusions / 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) Amanita phalloides (death cap) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||||||||
Authors | Boiero Sanders, M. / Oosterheert, W. / Hofnagel, O. / Bieling, P. / Raunser, S. | ||||||||||||
Funding support | Germany, European Union, 3items
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Citation | Journal: Nat Commun / Year: 2024 Title: Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly. Authors: Micaela Boiero Sanders / Wout Oosterheert / Oliver Hofnagel / Peter Bieling / Stefan Raunser / Abstract: Actin filament turnover involves subunits binding to and dissociating from the filament ends, with the pointed end being the primary site of filament disassembly. Several molecules modulate filament ...Actin filament turnover involves subunits binding to and dissociating from the filament ends, with the pointed end being the primary site of filament disassembly. Several molecules modulate filament turnover, but the underlying mechanisms remain incompletely understood. Here, we present three cryo-EM structures of the F-actin pointed end in the presence and absence of phalloidin or DNase I. The two terminal subunits at the undecorated pointed end adopt a twisted conformation. Phalloidin can still bind and bridge these subunits, inducing a conformational shift to a flattened, F-actin-like state. This explains how phalloidin prevents depolymerization at the pointed end. Interestingly, two DNase I molecules simultaneously bind to the phalloidin-stabilized pointed end. In the absence of phalloidin, DNase I binding would disrupt the terminal actin subunit packing, resulting in filament disassembly. Our findings uncover molecular principles of pointed end regulation and provide structural insights into the kinetic asymmetry between the actin filament ends. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fjm.cif.gz | 265.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fjm.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 9fjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fjm_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 9fjm_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 9fjm_validation.xml.gz | 65.1 KB | Display | |
Data in CIF | 9fjm_validation.cif.gz | 92.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/9fjm ftp://data.pdbj.org/pub/pdb/validation_reports/fj/9fjm | HTTPS FTP |
-Related structure data
Related structure data | 50506MC 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: 41632.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Beta-actin recombinantly purified from insect cells. Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Plasmid: p2336 pFL_ACTB_C272A / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709 #2: Protein/peptide | Type: Peptide-like / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: phalloidin from Amanita phalloides. / Source: (natural) Amanita phalloides (death cap) / References: BIRD: PRD_002366 #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-PO4 / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: BTI-Tnao38 | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.1 Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 286 K / Details: 3 seconds, force 0. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20393 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Details: Gatan energy filter. / Energyfilter slit width: 15 eV Spherical aberration corrector: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5200600 / Details: Particles picked using SPHIRE-crYOLO. | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280802 / Details: Local Refinement in CryoSPARC. / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8rtt Accession code: 8rtt / Details: actin and phalloidin model / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
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