|Entry||Database: PDB / ID: 7mgm|
|Title||Structure of yeast cytoplasmic dynein with AAA3 Walker B mutation bound to Lis1|
|Keywords||MOTOR PROTEIN / motor / AAA|
|Function / homology|
Function and homology information
microtubule sliding / microtubule organizing center organization / positive regulation of microtubule plus-end binding / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / microtubule plus-end binding / dynein complex / nuclear migration / dynein complex binding ...microtubule sliding / microtubule organizing center organization / positive regulation of microtubule plus-end binding / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / microtubule plus-end binding / dynein complex / nuclear migration / dynein complex binding / microtubule associated complex / establishment of mitotic spindle orientation / microtubule-based movement / cytoplasmic microtubule / 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 / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain, linker / Dynein heavy chain AAA lid domain / Dynein heavy chain, N-terminal region 2 ...Dynein regulator LIS1 / LIS1, N-terminal / Dynein heavy chain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain, linker / Dynein heavy chain AAA lid domain / Dynein heavy chain, N-terminal region 2 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain, linker, subdomain 3 / Hydrolytic ATP binding site of dynein motor region / Dynein heavy chain region D6 P-loop domain / Microtubule-binding stalk of dynein motor / Dynein heavy chain, AAA module D4 / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain AAA lid domain / Dynein heavy chain, coiled coil stalk / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / 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
Dynein heavy chain, cytoplasmic / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Nuclear distribution protein PAC1
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å|
|Authors||Lahiri, I. / Reimer, J.M. / Leschziner, A.E.|
|Funding support|| United States, 1items |
|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.
|Structure viewer||Molecule: |
Downloads & links
A: dynein AAA3-WalkerB mutant (E2488Q)
C: Nuclear distribution protein PAC1
B: Nuclear distribution protein PAC1
|#1: Protein|| |
Mass: 331524.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A0A7I9C1Z7
Mass: 57030.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P39946
Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
|#4: Chemical|| ChemComp-ADP / ||#5: Chemical||Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Complex of yeast dynein bound by two Lis1s in the presence of ATP-Va|
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Saccharomyces cerevisiae (baker's yeast)|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
Details: The yeast dynein was biotinylated prior to complex formation.
|Specimen support||Details: Quantifoil R2/2 grids with gold foil were used. A monolayer of streptavidin crystals was deposited prior to applying the sample. The streptavidin monolayer acted as an affinity surface for ...Details: Quantifoil R2/2 grids with gold foil were used. A monolayer of streptavidin crystals was deposited prior to applying the sample. The streptavidin monolayer acted as an affinity surface for the biotinylated sample.|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2700 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K|
|Image recording||Average exposure time: 10 sec. / Electron dose: 58.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2229|
|Image scans||Movie frames/image: 50 / Used frames/image: 1-50|
|Software||Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83975 / Symmetry type: POINT|
|Refine LS restraints|
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