- EMDB-6017: Dynein motor domain with truncated linker in complex with Lis1 in... -
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Basic information
Entry
Database: EMDB / ID: EMD-6017
Title
Dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide
Map data
Reconstruction of dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide
Sample
Sample: Dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide
Protein or peptide: Dynein heavy chain
Protein or peptide: Lis1
Keywords
dynein / lis1 / regulation mechanism
Function / homology
Function and homology information
positive regulation of microtubule plus-end binding / microtubule sliding / karyogamy / microtubule organizing center organization / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding ...positive regulation of microtubule plus-end binding / microtubule sliding / karyogamy / microtubule organizing center organization / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / vesicle transport along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule plus-end binding / spindle pole body / cytoplasmic dynein complex / retrograde axonal transport / nuclear migration / microtubule associated complex / dynein intermediate chain binding / dynein complex binding / cytoplasmic microtubule / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic microtubule organization / Neutrophil degranulation / 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
Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain ...Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / P-loop containing dynein motor region / 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
Journal: Elife / Year: 2014 Title: Lis1 regulates dynein by sterically blocking its mechanochemical cycle. Authors: Katerina Toropova / Sirui Zou / Anthony J Roberts / William B Redwine / Brian S Goodman / Samara L Reck-Peterson / Andres E Leschziner / Abstract: Regulation of cytoplasmic dynein's motor activity is essential for diverse eukaryotic functions, including cell division, intracellular transport, and brain development. The dynein regulator Lis1 is ...Regulation of cytoplasmic dynein's motor activity is essential for diverse eukaryotic functions, including cell division, intracellular transport, and brain development. The dynein regulator Lis1 is known to keep dynein bound to microtubules; however, how this is accomplished mechanistically remains unknown. We have used three-dimensional electron microscopy, single-molecule imaging, biochemistry, and in vivo assays to help establish this mechanism. The three-dimensional structure of the dynein-Lis1 complex shows that binding of Lis1 to dynein's AAA+ ring sterically prevents dynein's main mechanical element, the 'linker', from completing its normal conformational cycle. Single-molecule experiments show that eliminating this block by shortening the linker to a point where it can physically bypass Lis1 renders single dynein motors insensitive to regulation by Lis1. Our data reveal that Lis1 keeps dynein in a persistent microtubule-bound state by directly blocking the progression of its mechanochemical cycle.
History
Deposition
Aug 4, 2014
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Header (metadata) release
Sep 24, 2014
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Map release
Nov 19, 2014
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Update
Nov 19, 2014
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Current status
Nov 19, 2014
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Dynein motor domain with truncated linker in complex with Lis1 in...
Entire
Name: Dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide
Components
Sample: Dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide
Protein or peptide: Dynein heavy chain
Protein or peptide: Lis1
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Supramolecule #1000: Dynein motor domain with truncated linker in complex with Lis1 in...
Supramolecule
Name: Dynein motor domain with truncated linker in complex with Lis1 in the absence of nucleotide type: sample / ID: 1000 Oligomeric state: One motor domain to one Lis1 propeller domain Number unique components: 2
Molecular weight
Experimental: 428 KDa / Theoretical: 428 KDa
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Macromolecule #1: Dynein heavy chain
Macromolecule
Name: Dynein heavy chain / type: protein_or_peptide / ID: 1 / Name.synonym: DYN1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Name: Lis1 / type: protein_or_peptide / ID: 2 / Name.synonym: Pac1 / Details: Only a single copy of Lis1 is resolved in the map. / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
pH: 8 Details: 50 mM Tris-HCl, 150 mM potassium acetate, 2 mM magnesium acetate, 1 mM EGTA, 1 mM DTT, 0.14 U/ml apyrase
Staining
Type: NEGATIVE Details: Grids with adsorbed protein were floated on 2% w/v uranyl formate, then sandwiched with a thin layer of carbon, blotted, and frozen in liquid nitrogen.
Grid
Details: 200 mesh C-flat grid with thin carbon support
Vitrification
Cryogen name: NITROGEN / Instrument: OTHER Method: Manually blot, wait 10-20 seconds, then manually plunge into liquid nitrogen.
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Electron microscopy
Microscope
FEI TECNAI 20
Date
Feb 24, 2014
Image recording
Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 25 e/Å2
Electron beam
Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
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