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Yorodumi- EMDB-19499: Structure of the F-actin barbed end bound by Cdc12 and profilin (... -
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Open data
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Basic information
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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 | ||||||||||||
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Keywords | actin / formin / Cdc12 / profilin / actin assembly / STRUCTURAL PROTEIN | ||||||||||||
| Function / homology | Function and homology informationprotein localization to mitotic actomyosin contractile ring / F-bar domain binding / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...protein localization to mitotic actomyosin contractile ring / F-bar domain binding / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / negative regulation of actin filament bundle assembly / DNA-methyltransferase activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / bBAF complex / cellular response to cytochalasin B / regulation of actin filament polymerization / npBAF complex / Signaling by ROBO receptors / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / barbed-end actin filament capping / GBAF complex / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / positive regulation of ATP-dependent activity / Tat protein binding / postsynaptic actin cytoskeleton / DNA alkylation repair / mating projection tip / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / proline-rich region binding / regulation of double-strand break repair / regulation of nucleotide-excision repair / PCP/CE pathway / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / positive regulation of ruffle assembly / Sensory processing of sound by outer hair cells of the cochlea / negative regulation of stress fiber assembly / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / apical junction complex / cell division site / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / positive regulation of actin filament polymerization / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / brush border / regulation of G1/S transition of mitotic cell cycle / actin filament bundle assembly / positive regulation of epithelial cell migration / actin monomer binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / kinesin binding / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / actin filament polymerization / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / methyltransferase activity Similarity search - Function | ||||||||||||
| Biological species | Homo sapiens (human) / ![]() 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: 2024Title: 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. | ||||||||||||
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Structure visualization
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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 ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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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 |
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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 |
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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.. |
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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 |
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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: |
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About Yorodumi



Keywords
Homo sapiens (human)
Amanita phalloides (death cap)
Authors
Germany, European Union, 3 items
Citation


























Z (Sec.)
Y (Row.)
X (Col.)




















































Trichoplusia ni (cabbage looper)


FIELD EMISSION GUN


