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Yorodumi- EMDB-11315: The pointed end complex of dynactin, with accompanying Arp1/actin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11315 | |||||||||
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Title | The pointed end complex of dynactin, with accompanying Arp1/actin filament subunits | |||||||||
Map data | Map has been fitted using EMDA to EMD-11313 | |||||||||
Sample |
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Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.05 Å | |||||||||
Authors | Lau CK / Lacey SE / Carter AP | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Authors: Clinton K Lau / Francis J O'Reilly / Balaji Santhanam / Samuel E Lacey / Juri Rappsilber / Andrew P Carter / Abstract: Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled- ...Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end. | |||||||||
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_11315.map.gz | 178.1 MB | EMDB map data format | |
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Header (meta data) | emd-11315-v30.xml emd-11315.xml | 26.6 KB 26.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11315_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_11315.png | 49.8 KB | ||
Masks | emd_11315_msk_1.map | 307.5 MB | Mask map | |
Others | emd_11315_additional_1.map.gz emd_11315_additional_2.map.gz emd_11315_additional_3.map.gz emd_11315_half_map_1.map.gz emd_11315_half_map_2.map.gz | 62.7 MB 62.4 MB 230 KB 51.8 MB 51.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11315 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11315 | HTTPS FTP |
-Validation report
Summary document | emd_11315_validation.pdf.gz | 309.5 KB | Display | EMDB validaton report |
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Full document | emd_11315_full_validation.pdf.gz | 308.6 KB | Display | |
Data in XML | emd_11315_validation.xml.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11315 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11315 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11315.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map has been fitted using EMDA to EMD-11313 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11315_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Same map as main map, before fitting.
File | emd_11315_additional_1.map | ||||||||||||
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Annotation | Same map as main map, before fitting. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map postprocessed from half maps, sharpened manually using...
File | emd_11315_additional_2.map | ||||||||||||
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Annotation | Map postprocessed from half maps, sharpened manually using b factor of -80 for assist connectivity of chains. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Mask aligned to the main map, before fitting.
File | emd_11315_additional_3.map | ||||||||||||
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Annotation | Mask aligned to the main map, before fitting. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11315_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11315_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dynactin complex
Entire | Name: Dynactin complex |
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Components |
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-Supramolecule #1: Dynactin complex
Supramolecule | Name: Dynactin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17 |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 1 MDa |