+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4269 | |||||||||
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Title | Abp1-SNAP bound to Arp2/3 complex (class 1) | |||||||||
Map data | Abp1-SNAP bound to Arp2/3 complex (class 1) | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Sokolova OS / Goode BL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF. Authors: Siyang Guo / Olga S Sokolova / Johnson Chung / Shae Padrick / Jeff Gelles / Bruce L Goode / Abstract: Formation and turnover of branched actin networks underlies cell migration and other essential force-driven processes. Type I nucleation-promoting factors (NPFs) such as WASP recruit actin monomers ...Formation and turnover of branched actin networks underlies cell migration and other essential force-driven processes. Type I nucleation-promoting factors (NPFs) such as WASP recruit actin monomers to Arp2/3 complex to stimulate nucleation. In contrast, mechanisms of type II NPFs such as Abp1 (also known as HIP55 and Drebrin-like protein) are less well understood. Here, we use single-molecule analysis to investigate yeast Abp1 effects on Arp2/3 complex, and find that Abp1 strongly enhances Arp2/3-dependent branch nucleation by stabilizing Arp2/3 on sides of mother filaments. Abp1 binds dynamically to filament sides, with sub-second lifetimes, yet associates stably with branch junctions. Further, we uncover a role for Abp1 in protecting filament junctions from GMF-induced debranching by competing with GMF for Arp2/3 binding. These data, combined with EM structures of Abp1 dimers bound to Arp2/3 complex in two different conformations, expand our mechanistic understanding of type II NPFs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4269.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-4269-v30.xml emd-4269.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | emd_4269.png | 50.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4269 | HTTPS FTP |
-Validation report
Summary document | emd_4269_validation.pdf.gz | 202.4 KB | Display | EMDB validaton report |
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Full document | emd_4269_full_validation.pdf.gz | 201.5 KB | Display | |
Data in XML | emd_4269_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4269 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4269 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4269.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Abp1-SNAP bound to Arp2/3 complex (class 1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Arp2/3 complex with bound Abp1 dimer
Entire | Name: Arp2/3 complex with bound Abp1 dimer |
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Components |
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-Supramolecule #1: Arp2/3 complex with bound Abp1 dimer
Supramolecule | Name: Arp2/3 complex with bound Abp1 dimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: 0.75% uranium formiate |
-Electron microscopy
Microscope | JEOL 2100 |
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Image recording | Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 13.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2500 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |