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Yorodumi- EMDB-15139: Tomogram of a lamellipodium of an ArpC5 knockout B16-F1 mouse mel... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15139 | |||||||||
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Title | Tomogram of a lamellipodium of an ArpC5 knockout B16-F1 mouse melanoma cell | |||||||||
Map data | Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse melanoma cell | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Faessler F / Javoor MG / Datler J / Doering H / Hofer FW / Dimchev G / Hodirnau VV / Rottner K / Schur FKM | |||||||||
Funding support | Austria, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning. Authors: Florian Fäßler / Manjunath G Javoor / Julia Datler / Hermann Döring / Florian W Hofer / Georgi Dimchev / Victor-Valentin Hodirnau / Jan Faix / Klemens Rottner / Florian K M Schur / Abstract: Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. ...Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform-specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15139.map.gz | 260.5 MB | EMDB map data format | |
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Header (meta data) | emd-15139-v30.xml emd-15139.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_15139.png | 246.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15139 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15139 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15139.map.gz / Format: CCP4 / Size: 281.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse melanoma cell | ||||||||||||||||||||
Voxel size | X=Y=Z: 13.544 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse mela...
Entire | Name: Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse melanoma cell |
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Components |
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-Supramolecule #1: Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse mela...
Supramolecule | Name: Tomogram of a lamellipodium of a ArpC5 knockout B16-F1 mouse melanoma cell type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: B16-F1 / Tissue: Melanoma |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6.2 Component:
Details: Adjust to pH 6.2 using NaOH Immediately prior to use, add Phalloidin to a final concentration of 1ug/ml | ||||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR Details: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Laminin for 60min | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP | ||||||||||||||
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 53000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 61 / Average electron dose: 2.79 e/Å2 Details: Images were collected in movie-mode with 8 frames per tilt |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: RELION (ver. 3.0.8) / Number images used: 59 |
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