+Open data
-Basic information
Entry | Database: PDB / ID: 8ru2 | ||||||||||||
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Title | Structure of the F-actin barbed end bound by formin mDia1 | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / actin / formin / Cdc12 / profilin / actin assembly | ||||||||||||
Function / homology | Function and homology information MGMT-mediated DNA damage reversal / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...MGMT-mediated DNA damage reversal / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / actin nucleation / RHOA GTPase cycle / neuron projection retraction / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / DNA-methyltransferase activity / morphogenesis of a polarized epithelium / RHO GTPases Activate Formins / bBAF complex / profilin binding / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / 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 / DNA ligation / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / DNA alkylation repair / regulation of microtubule-based process / RHOF GTPase cycle / Adherens junctions interactions / tight junction / axon midline choice point recognition / 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 / synaptic vesicle endocytosis / positive regulation of double-strand break repair via homologous recombination / ephrin receptor signaling pathway / 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 / cytoskeleton organization / substantia nigra development / EPHB-mediated forward signaling / actin filament polymerization / Neutrophil degranulation / axonogenesis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / platelet aggregation / negative regulation of protein binding / methyltransferase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / adherens junction / sensory perception of sound / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||||||||
Authors | Oosterheert, W. / Boiero Sanders, M. / Funk, J. / Prumbaum, D. / Raunser, S. / Bieling, P. | ||||||||||||
Funding support | Germany, European Union, 3items
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Citation | Journal: Science / Year: 2024 Title: Molecular mechanism of actin filament elongation by formins. Authors: Wout Oosterheert / Micaela Boiero Sanders / Johanna Funk / Daniel Prumbaum / Stefan Raunser / Peter Bieling / Abstract: Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action ...Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ru2.cif.gz | 346.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ru2.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ru2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ru2_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8ru2_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8ru2_validation.xml.gz | 72.3 KB | Display | |
Data in CIF | 8ru2_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/8ru2 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/8ru2 | HTTPS FTP |
-Related structure data
Related structure data | 19503MC 8rttC 8rtyC 8ru0C 8rv2C C: citing same article (ref.) M: map data used to model this data |
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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: 41632.422 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Human beta-actin was recombinantly purified from BTI-Tnao38 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 | Mass: 86469.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Has a N-terminal snap-tag. Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse) Gene: MGMT, Diaph1, Diap1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star pRARE References: UniProt: P16455, UniProt: O08808, methylated-DNA-[protein]-cysteine S-methyltransferase #3: Chemical | #4: Chemical | 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 | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.1 | ||||||||||||||||||||||||||||
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: 67.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 38913 |
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: 1963686 / Details: Particles picked using SPHIRE-crYOLO. | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150807 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: Refinement performed using phenix real-space refine | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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