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Yorodumi- EMDB-3706: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3706 | |||||||||
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Title | Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2 | |||||||||
Map data | 3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered. | |||||||||
Sample |
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Function / homology | Function and homology information kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / F-actin capping protein complex / dense body / Neutrophil degranulation / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / coronary vasculature development ...kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / F-actin capping protein complex / dense body / Neutrophil degranulation / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / coronary vasculature development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / aorta development / ventricular septum development / dynein complex binding / endoplasmic reticulum to Golgi vesicle-mediated transport / microtubule-based process / 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 / kinetochore / antigen processing and presentation of exogenous peptide antigen via MHC class II / actin binding / cell cortex / actin cytoskeleton organization / nuclear membrane / cytoskeleton / focal adhesion / centrosome / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 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_3706.map.gz | 9.3 MB | EMDB map data format | |
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Header (meta data) | emd-3706-v30.xml emd-3706.xml | 66.9 KB 66.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3706_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_3706.png | 124.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3706 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3706 | HTTPS FTP |
-Related structure data
Related structure data | 5nw4MC 3698C 3703C 3704C 3705C 3707C 5nugC 5nvsC 5nvuC C: citing same article (ref.) M: atomic model generated by this map |
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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_3706.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co...
+Supramolecule #1: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co...
+Supramolecule #2: dynein-1
+Supramolecule #3: dynactin
+Supramolecule #4: BICD2
+Macromolecule #1: dynein heavy chain
+Macromolecule #2: dynein intermediate chain
+Macromolecule #3: dynein intermediate chain
+Macromolecule #4: dynein heavy chain
+Macromolecule #5: dynein N-terminal dimerization domain
+Macromolecule #6: dynein N-terminal dimerization domain
+Macromolecule #7: Robl
+Macromolecule #8: dynein light intermediate chain
+Macromolecule #9: dynein light intermediate chain
+Macromolecule #10: Arp1
+Macromolecule #11: beta-actin
+Macromolecule #12: Arp11
+Macromolecule #13: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #14: F-actin capping protein beta subunit variant II
+Macromolecule #15: dynactin shoulder complex
+Macromolecule #16: dynactin shoulder complex
+Macromolecule #17: dynactin shoulder complex
+Macromolecule #18: dynactin shoulder complex
+Macromolecule #19: Dynactin 6
+Macromolecule #20: Dynactin subunit 5
+Macromolecule #21: dynactin pointed end p62
+Macromolecule #22: p150
+Macromolecule #23: Dynactin
+Macromolecule #24: Dynactin
+Macromolecule #25: Dynactin
+Macromolecule #26: Dynactin
+Macromolecule #27: dynactin p150
+Macromolecule #28: BICD2N
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |