- EMDB-25497: Signal-subtracted reconstruction of yeast cytoplasmic dynein-1 (A... -
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Basic information
Entry
Database: EMDB / ID: EMD-25497
Title
Signal-subtracted reconstruction of yeast cytoplasmic dynein-1 (AAA3 Walker B mutant, E2488Q) AAA2-AAA5L domains bound to Lis1
Map data
Signal subtracted reconstruction of AAA2-AAA5L domains of yeast cytoplasmic dynein 1 (E2488Q) with Lis1.
Sample
Complex: Complex of yeast dynein bound by two Lis1s in the presence of ATP-Va
Protein or peptide: cytoplasmic dynein AAA3-WalkerB mutant (E2488Q)
Function / homology
Function and homology information
microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / dynein complex / minus-end-directed microtubule motor activity / microtubule plus-end binding / nuclear migration / microtubule associated complex / dynein complex binding ...microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / vesicle transport along microtubule / dynein complex / minus-end-directed microtubule motor activity / microtubule plus-end binding / nuclear migration / microtubule associated complex / dynein complex binding / microtubule-based movement / cytoplasmic microtubule / establishment of mitotic spindle orientation / Antigen processing: Ubiquitination & Proteasome degradation / kinetochore / spindle pole / nuclear envelope / microtubule / cell division / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function
Dynein regulator LIS1 / LIS1, N-terminal / : / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker ...Dynein regulator LIS1 / LIS1, N-terminal / : / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM107214
United States
Citation
Journal: Elife / Year: 2022 Title: Structural basis for cytoplasmic dynein-1 regulation by Lis1. Authors: John P Gillies / Janice M Reimer / Eva P Karasmanis / Indrajit Lahiri / Zaw Min Htet / Andres E Leschziner / Samara L Reck-Peterson / Abstract: The lissencephaly 1 gene, , is mutated in patients with the neurodevelopmental disease lissencephaly. The Lis1 protein is conserved from fungi to mammals and is a key regulator of cytoplasmic dynein- ...The lissencephaly 1 gene, , is mutated in patients with the neurodevelopmental disease lissencephaly. The Lis1 protein is conserved from fungi to mammals and is a key regulator of cytoplasmic dynein-1, the major minus-end-directed microtubule motor in many eukaryotes. Lis1 is the only dynein regulator known to bind directly to dynein's motor domain, and by doing so alters dynein's mechanochemistry. Lis1 is required for the formation of fully active dynein complexes, which also contain essential cofactors: dynactin and an activating adaptor. Here, we report the first high-resolution structure of the yeast dynein-Lis1 complex. Our 3.1 Å structure reveals, in molecular detail, the major contacts between dynein and Lis1 and between Lis1's ß-propellers. Structure-guided mutations in Lis1 and dynein show that these contacts are required for Lis1's ability to form fully active human dynein complexes and to regulate yeast dynein's mechanochemistry and in vivo function.
History
Deposition
Nov 22, 2021
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Header (metadata) release
Jan 19, 2022
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Map release
Jan 19, 2022
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Update
Jan 19, 2022
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Current status
Jan 19, 2022
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK II
Details
Yeast dynein was biotinylated prior to complex formation.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Temperature
Min: 70.0 K / Max: 70.0 K
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2229 / Average exposure time: 10.0 sec. / Average electron dose: 58.3 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF Details: Particles were signal subtracted and recentered in Relion 3.1. The mask used during signal subtraction was placed around AAA2-AAA5L and both Lis1s. Local refinement was carried out in cryoSPARC. Number images used: 83975
Initial angle assignment
Type: RANDOM ASSIGNMENT
Final angle assignment
Type: PROJECTION MATCHING
FSC plot (resolution estimation)
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