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Yorodumi- EMDB-3707: Locally refined human cytoplasmic dynein-1 tail bound to dynactin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3707 | |||||||||
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Title | Locally refined human cytoplasmic dynein-1 tail bound to dynactin and an N-terminal construct of BICD2 | |||||||||
Map data | Focused refinement of the dynein tail improved its density near the LIC binding site. | |||||||||
Sample |
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Function / homology | Function and homology information kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / 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 / F-actin capping protein complex ...kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / 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 / F-actin capping protein complex / negative regulation of filopodium assembly / dense body / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / coronary vasculature development / barbed-end actin filament capping / regulation of lamellipodium assembly / aorta development / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / ventricular septum development / COPI-mediated anterograde transport / dynein complex binding / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / axon cytoplasm / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitotic spindle organization / cell morphogenesis / kinetochore / antigen processing and presentation of exogenous peptide antigen via MHC class II / actin filament binding / cell cortex / actin cytoskeleton organization / nuclear membrane / cytoskeleton / focal adhesion / centrosome / nucleoplasm / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Zhang K / Foster HE / Carter AP | |||||||||
Citation | Journal: Cell / Year: 2017 Title: Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Authors: Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter / Abstract: Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves ...Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity. | |||||||||
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_3707.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-3707-v30.xml emd-3707.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3707_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_3707.png | 86.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3707 | HTTPS FTP |
-Validation report
Summary document | emd_3707_validation.pdf.gz | 222.2 KB | Display | EMDB validaton report |
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Full document | emd_3707_full_validation.pdf.gz | 221.3 KB | Display | |
Data in XML | emd_3707_validation.xml.gz | 11.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3707 | HTTPS FTP |
-Related structure data
Related structure data | 3698C 3703C 3704C 3705C 3706C 5nugC 5nvsC 5nvuC 5nw4C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3707.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused refinement of the dynein tail improved its density near the LIC binding site. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.68 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 : Locally refined human cytoplasmic dynein-1 tail bound to dynactin...
Entire | Name: Locally refined human cytoplasmic dynein-1 tail bound to dynactin and an N-terminal construct of BICD2 |
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Components |
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-Supramolecule #1: Locally refined human cytoplasmic dynein-1 tail bound to dynactin...
Supramolecule | Name: Locally refined human cytoplasmic dynein-1 tail bound to dynactin and an N-terminal construct of BICD2 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 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 |