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Yorodumi- EMDB-14556: Cytoplasmic dynein light intermediate chain (B1) bound to the mot... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14556 | ||||||||||||
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Title | Cytoplasmic dynein light intermediate chain (B1) bound to the motor domain (A2). | ||||||||||||
Map data | Dynein-B1 light intermediate chain bound to the dynein-A2 motor domain. | ||||||||||||
Sample |
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Function / homology | Function and homology information dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex ...dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / nuclear migration / centrosome localization / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / microtubule cytoskeleton organization / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / late endosome / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||
Authors | Chaaban S / Carter AP | ||||||||||||
Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Nature / Year: 2022 Title: Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Authors: Sami Chaaban / Andrew P Carter / Abstract: Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between ...Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour. Different coiled-coil adaptors are linked to different cargos, and some share motifs known to contact sites on dynein and dynactin. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14556.map.gz | 106.5 MB | EMDB map data format | |
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Header (meta data) | emd-14556-v30.xml emd-14556.xml | 28.1 KB 28.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14556_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_14556.png | 63.3 KB | ||
Masks | emd_14556_msk_1.map | 113.6 MB | Mask map | |
Others | emd_14556_half_map_1.map.gz emd_14556_half_map_2.map.gz | 89.2 MB 89.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14556 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14556 | HTTPS FTP |
-Related structure data
Related structure data | 7z8lMC 7z8fC 7z8gC 7z8hC 7z8iC 7z8jC 7z8kC 7z8mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14556.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Dynein-B1 light intermediate chain bound to the dynein-A2 motor domain. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.03781 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14556_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the dynein-B1 light intermediate...
File | emd_14556_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of the dynein-B1 light intermediate chain bound to the dynein-A2 motor domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the dynein-B1 light intermediate...
File | emd_14556_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of the dynein-B1 light intermediate chain bound to the dynein-A2 motor domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of dynein, dynactin, and BICDR1 bound to microtubules
+Supramolecule #1: Complex of dynein, dynactin, and BICDR1 bound to microtubules
+Supramolecule #2: Dynein, cytoplasmic 1
+Supramolecule #3: Dynactin
+Supramolecule #4: BICDR1
+Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #2: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 20 second incubation. |
-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: 1.2 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / 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 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 14 / Number real images: 88715 / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2 Details: Images were collected in movie-mode and fractionated into 53 movie frames |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7z8l: |