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Yorodumi- EMDB-19499: Structure of the F-actin barbed end bound by Cdc12 and profilin (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19499 | ||||||||||||
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Title | Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom | ||||||||||||
Map data | Sharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
Sample |
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Keywords | actin / formin / Cdc12 / profilin / actin assembly / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / MGMT-mediated DNA damage reversal / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / MGMT-mediated DNA damage reversal / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / regulation of transepithelial transport / DNA-methyltransferase activity / 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 / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / Signaling by ROBO receptors / regulation of actin filament polymerization / 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 / mating projection tip / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / barbed-end actin filament capping / DNA alkylation repair / RSC-type complex / Prefoldin mediated transfer of substrate to CCT/TriC / RHOF GTPase cycle / positive regulation of ATP-dependent activity / Adherens junctions interactions / proline-rich region binding / tight junction / PCP/CE pathway / positive regulation of ruffle assembly / 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 / negative regulation of stress fiber assembly / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of actin filament polymerization / cortical cytoskeleton / maintenance of blood-brain barrier / cell division site / positive regulation of stem cell population maintenance / positive regulation of epithelial cell migration / 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 / actin filament bundle assembly / calyx of Held / negative regulation of cell differentiation / actin monomer binding / 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 / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / EPHB-mediated forward signaling / actin filament polymerization / phosphotyrosine residue binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / axonogenesis / platelet aggregation Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Schizosaccharomyces pombe (fission yeast) / Amanita phalloides (death cap) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.25 Å | ||||||||||||
Authors | Oosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P | ||||||||||||
Funding support | Germany, European Union, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19499.map.gz | 398.4 MB | EMDB map data format | |
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Header (meta data) | emd-19499-v30.xml emd-19499.xml | 30.9 KB 30.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19499_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_19499.png | 90.2 KB | ||
Masks | emd_19499_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-19499.cif.gz | 8.7 KB | ||
Others | emd_19499_additional_1.map.gz emd_19499_half_map_1.map.gz emd_19499_half_map_2.map.gz | 206.5 MB 392 MB 392 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19499 | HTTPS FTP |
-Validation report
Summary document | emd_19499_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_19499_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_19499_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | emd_19499_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19499 | HTTPS FTP |
-Related structure data
Related structure data | 8rtyMC 8rttC 8ru0C 8ru2C 8rv2C C: citing same article (ref.) M: atomic model generated by this map |
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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_19499.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19499_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: 3D-refined, unsharpened cryo-EM density map of the F-actin...
File | emd_19499_additional_1.map | ||||||||||||
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Annotation | 3D-refined, unsharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2 of the F-actin barbed...
File | emd_19499_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 2 of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1 of the F-actin barbed...
File | emd_19499_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 1 of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...
+Supramolecule #1: Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...
+Supramolecule #2: Actin filament
+Supramolecule #3: Dimeric FH1FH2 domain of S. Pombe Cdc12
+Supramolecule #4: Profilin-1-S29C/S71M
+Supramolecule #5: Phalloidin
+Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed
+Macromolecule #2: Methylated-DNA--protein-cysteine methyltransferase,Cell division ...
+Macromolecule #3: Phalloidin (Amanita phalloides)
+Macromolecule #4: Profilin-1
+Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: PHOSPHATE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 Component:
Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) | ||||||||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds, force 0.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV / Details: Gatan energy filter. |
Details | 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5287 / Average electron dose: 63.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Refinement performed using phenix real-space refine | |||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | |||||||||
Output model | PDB-8rty: |