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- PDB-8e00: Symmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8 | |||||||||
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Title | Symmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in the chi conformation. | |||||||||
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![]() | MOTOR PROTEIN / dynein / transport | |||||||||
Function / homology | ![]() positive regulation of microtubule plus-end binding / microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule plus-end binding / cytoplasmic dynein complex / retrograde axonal transport ...positive regulation of microtubule plus-end binding / microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule plus-end binding / cytoplasmic dynein complex / retrograde axonal transport / nuclear migration / microtubule associated complex / dynein intermediate chain binding / dynein complex binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic microtubule organization / mitotic spindle organization / kinetochore / spindle pole / nuclear envelope / cell cortex / cell division / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Reimer, J.M. / Lahiri, I. / Leschziner, A.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge. Authors: Eva P Karasmanis / Janice M Reimer / Agnieszka A Kendrick / Kendrick H V Nguyen / Jennifer A Rodriguez / Joey B Truong / Indrajit Lahiri / Samara L Reck-Peterson / Andres E Leschziner / ![]() ![]() Abstract: Cytoplasmic dynein-1 transports intracellular cargo towards microtubule minus ends. Dynein is autoinhibited and undergoes conformational changes to form an active complex that consists of one or two ...Cytoplasmic dynein-1 transports intracellular cargo towards microtubule minus ends. Dynein is autoinhibited and undergoes conformational changes to form an active complex that consists of one or two dynein dimers, the dynactin complex, and activating adapter(s). The Lissencephaly 1 gene, LIS1, is genetically linked to the dynein pathway from fungi to mammals and is mutated in people with the neurodevelopmental disease lissencephaly. Lis1 is required for active dynein complexes to form, but how it enables this is unclear. Here, we present a structure of two yeast dynein motor domains with two Lis1 dimers wedged in-between. The contact sites between dynein and Lis1 in this structure, termed 'Chi,' are required for Lis1's regulation of dynein in Saccharomyces cerevisiae in vivo and the formation of active human dynein-dynactin-activating adapter complexes in vitro. We propose that this structure represents an intermediate in dynein's activation pathway, revealing how Lis1 relieves dynein's autoinhibited state. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 573.2 KB | Display | ![]() |
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PDB format | ![]() | 449.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 88.7 KB | Display | |
Data in CIF | ![]() | 134.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27811MC ![]() 8dzzC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 331524.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 100% identical to UniParc UPI0005D9E17C Source: (gene. exp.) ![]() ![]() Gene: DYN1, GI527_G0003698 / Production host: ![]() ![]() | ||||||||
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#2: Protein | Mass: 57030.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PAC1, LIS1, YOR269W / Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-ADP / | Has ligand of interest | Y | Sequence details | Dynein heavy chain, cytoplasmic sequence is 100% identical to UniParc UPI0005D9E17C | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: streptavidin affinity grids were used |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 58.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46770 / Symmetry type: POINT | ||||||||||||||||||||||||
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