[English] 日本語
Yorodumi- EMDB-4169: N terminal region of dynein tail domains in complex with dynactin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4169 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1 | |||||||||
Map data | Map of the N-terminal half of two dynein tail domains bound to dynactin and BICDR1. This map was generated after particle signal subtraction from the overall map (separate deposition) | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / transport along microtubule / WASH complex / F-actin capping protein complex / positive regulation of intracellular transport / dynein light chain binding / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / positive regulation of spindle assembly / actin cortical patch / vesicle transport along microtubule / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / barbed-end actin filament capping / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / regulation of cell morphogenesis / nuclear migration / regulation of lamellipodium assembly / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / dynactin binding / microtubule-based process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / 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 / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / HCMV Early Events / cell morphogenesis / small GTPase binding / Aggrephagy / actin filament binding / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / neuron projection development / positive regulation of cold-induced thermogenesis / actin binding / cell cortex / actin cytoskeleton organization / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Mus musculus (house mouse) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Urnavicius L / Lau CK / Elshenawy MM / Morales-Rios E / Motz C / Yildiz A / Carter AP | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: Nature / Year: 2018 Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement. Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter / Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4169.map.gz | 288.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4169-v30.xml emd-4169.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
Images | emd_4169.png | 139 KB | ||
Others | emd_4169_additional_1.map.gz emd_4169_additional_2.map.gz | 1 MB 1.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4169 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4169 | HTTPS FTP |
-Validation report
Summary document | emd_4169_validation.pdf.gz | 226.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4169_full_validation.pdf.gz | 225.7 KB | Display | |
Data in XML | emd_4169_validation.xml.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4169 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4169 | HTTPS FTP |
-Related structure data
Related structure data | 6f1uMC 4168C 4170C 4171C 4172C 4177C 5owoC 6f1tC 6f1vC 6f1yC 6f1zC 6f38C 6f3aC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4169.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map of the N-terminal half of two dynein tail domains bound to dynactin and BICDR1. This map was generated after particle signal subtraction from the overall map (separate deposition) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Map of summed signal of dynein heavy chains present in main map
File | emd_4169_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map of summed signal of dynein heavy chains present in main map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Map of summed signal of dynein intermediate chains...
File | emd_4169_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map of summed signal of dynein intermediate chains present in main map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Two dynein tail domains bound to dynactin and BICDR1.
+Supramolecule #1: Two dynein tail domains bound to dynactin and BICDR1.
+Supramolecule #2: dynactin filament
+Supramolecule #3: Cytoplasmic dynein
+Supramolecule #4: BICDR1
+Macromolecule #1: ARP1 actin related protein 1 homolog A
+Macromolecule #2: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #3: F-actin capping protein beta subunit
+Macromolecule #4: Dynactin subunit 2
+Macromolecule #5: Dynactin subunit 2
+Macromolecule #6: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #7: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #8: BICD family-like cargo adapter 1
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Target criteria: Cross-correlation coefficient |
---|---|
Output model | PDB-6f1u: |