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- EMDB-14556: Cytoplasmic dynein light intermediate chain (B1) bound to the mot... -
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Open data
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Basic information
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Title | Cytoplasmic dynein light intermediate chain (B1) bound to the motor domain (A2). | ||||||||||||
![]() | Dynein-B1 light intermediate chain bound to the dynein-A2 motor domain. | ||||||||||||
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Function / homology | ![]() positive regulation of intracellular transport / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / dynein complex / P-body assembly / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity ...positive regulation of intracellular transport / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / dynein complex / P-body assembly / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / retrograde axonal transport / 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 / Mitotic Prometaphase / cytoplasmic microtubule organization / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / axon cytoplasm / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / kinetochore / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / 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 / identical protein binding / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||
![]() | Chaaban S / Carter AP | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 106.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.1 KB 28.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11 KB | Display | ![]() |
Images | ![]() | 63.3 KB | ||
Masks | ![]() | 113.6 MB | ![]() | |
Others | ![]() ![]() | 89.2 MB 89.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 862.5 KB | Display | ![]() |
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Full document | ![]() | 862 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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 |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7z8l: |