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- PDB-8e00: Symmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in... -

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Basic information

Entry
Database: PDB / ID: 8
TitleSymmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in the chi conformation.
Components
  • Dynein heavy chain, cytoplasmic
  • Nuclear distribution protein PAC1
KeywordsMOTOR PROTEIN / dynein / transport
Function / homology
Function and homology information


microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / microtubule plus-end binding / vesicle transport along microtubule / retrograde axonal transport / minus-end-directed microtubule motor activity / microtubule associated complex / dynein light intermediate chain binding / cytoplasmic dynein complex ...microtubule sliding / microtubule organizing center organization / nuclear migration along microtubule / microtubule plus-end binding / vesicle transport along microtubule / retrograde axonal transport / minus-end-directed microtubule motor activity / microtubule associated complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration / dynein complex binding / establishment of mitotic spindle orientation / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic microtubule / 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
Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain ...Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / 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 / WD domain, G-beta repeat / 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. / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynein heavy chain, cytoplasmic / Nuclear distribution protein PAC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsReimer, J.M. / Lahiri, I. / Leschziner, A.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2370-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107214 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
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
DepositionAug 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein heavy chain, cytoplasmic
B: Nuclear distribution protein PAC1
C: Nuclear distribution protein PAC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,5347
Polymers445,5853
Non-polymers1,9494
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dynein heavy chain, cytoplasmic / Dynein heavy chain / cytosolic


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.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DYN1, GI527_G0003698 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4FAJ6
#2: Protein Nuclear distribution protein PAC1 / Lissencephaly-1 homolog / LIS-1 / nudF homolog


Mass: 57030.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAC1, LIS1, YOR269W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39946
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN
Sequence detailsDynein heavy chain, cytoplasmic sequence is 100% identical to UniParc UPI0005D9E17C

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cytoplasmic dynein(E2448Q) bound to Lis1 in chi conformation
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: streptavidin affinity grids were used
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 58.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46770 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425353
ELECTRON MICROSCOPYf_angle_d0.71334317
ELECTRON MICROSCOPYf_dihedral_angle_d6.1733280
ELECTRON MICROSCOPYf_chiral_restr0.0483880
ELECTRON MICROSCOPYf_plane_restr0.0054300

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