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Yorodumi- EMDB-15947: Direct observation of the open conformational state of formin mDi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15947 | |||||||||
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Title | Direct observation of the open conformational state of formin mDia1 at actin filament barbed end | |||||||||
Map data | Actin barbed-end - Formin "Open State" | |||||||||
Sample |
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Keywords | Actin binding protein / Complex / barbed-end / formin / MOTOR PROTEIN | |||||||||
Biological species | Mus musculus (house mouse) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Maufront J / Guichard B / Cao L / Di Cicco A / Jegou A / Romet-Lemonne G / Bertin A | |||||||||
Funding support | France, 1 items
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Citation | Journal: Mol Biol Cell / Year: 2023 Title: Direct observation of the conformational states of formin mDia1 at actin filament barbed ends and along the filament. Authors: Julien Maufront / Bérengère Guichard / Lu-Yan Cao / Aurélie Di Cicco / Antoine Jégou / Guillaume Romet-Lemonne / Aurélie Bertin / Abstract: The fine regulation of actin polymerization is essential to control cell motility and architecture and to perform essential cellular functions. Formins are key regulators of actin filament assembly, ...The fine regulation of actin polymerization is essential to control cell motility and architecture and to perform essential cellular functions. Formins are key regulators of actin filament assembly, known to processively elongate filament barbed ends and increase their polymerization rate. Different models have been extrapolated to describe the molecular mechanism governing the processive motion of formin FH2 domains at polymerizing barbed ends. Using negative stain electron microscopy, we directly identified for the first time two conformations of the mDia1 formin FH2 domains in interaction with the barbed ends of actin filaments. These conformations agree with the speculated open and closed conformations of the "stair-stepping" model. We observed the FH2 dimers to be in the open conformation for 79% of the data, interacting with the two terminal actin subunits of the barbed end while they interact with three actin subunits in the closed conformation. In addition, we identified and characterized the structure of single FH2 dimers encircling the core of actin filaments, and reveal their ability to spontaneously depart from barbed ends. #1: Journal: BiorXiv / Year: 2022 Title: Direct observation of the open conformational state of formin mDia1 at actin filament barbed end Authors: Maufront J / Bertin A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15947.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-15947-v30.xml emd-15947.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15947_fsc.xml | 6 KB | Display | FSC data file |
Images | emd_15947.png | 39.3 KB | ||
Masks | emd_15947_msk_1.map | 22.2 MB | Mask map | |
Filedesc metadata | emd-15947.cif.gz | 4.4 KB | ||
Others | emd_15947_half_map_1.map.gz emd_15947_half_map_2.map.gz | 17 MB 17 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15947 | HTTPS FTP |
-Validation report
Summary document | emd_15947_validation.pdf.gz | 620.4 KB | Display | EMDB validaton report |
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Full document | emd_15947_full_validation.pdf.gz | 619.9 KB | Display | |
Data in XML | emd_15947_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_15947_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15947 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15947 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15947.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Actin barbed-end - Formin "Open State" | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.13 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15947_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Actin barbed-end - Formin "Open State"
File | emd_15947_half_map_1.map | ||||||||||||
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Annotation | Actin barbed-end - Formin "Open State" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Actin barbed-end - Formin "Open State"
File | emd_15947_half_map_2.map | ||||||||||||
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Annotation | Actin barbed-end - Formin "Open State" | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Actin barbed-end bound by formin mDia1 dimer in his "open state"
Entire | Name: Actin barbed-end bound by formin mDia1 dimer in his "open state" |
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Components |
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-Supramolecule #1: Actin barbed-end bound by formin mDia1 dimer in his "open state"
Supramolecule | Name: Actin barbed-end bound by formin mDia1 dimer in his "open state" type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: Formin mDia1 dimer
Supramolecule | Name: Formin mDia1 dimer / type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #3: Alpha Actin subunits assembled in helicoidal F-actin filament
Supramolecule | Name: Alpha Actin subunits assembled in helicoidal F-actin filament type: organelle_or_cellular_component / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation #1
Preparation ID | 1 |
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Concentration | 0.04 mg/mL |
Buffer | pH: 7.8 |
Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Sample preparation #2
Preparation ID | 2 |
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Concentration | 0.01 mg/mL |
Buffer | pH: 7.8 |
Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |