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- PDB-9dn7: CryoEM structures of yeast cytoplasmic dynein in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 9dn7
TitleCryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.
Components
  • Dynein heavy chain, cytoplasmic
  • Nuclear distribution protein PAC1
KeywordsMOTOR PROTEIN / Enzyme / AAA protein
Function / homology
Function and homology information


microtubule sliding / microtubule organizing center organization / karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / vesicle transport along microtubule / microtubule plus-end binding / spindle pole body / minus-end-directed microtubule motor activity ...microtubule sliding / microtubule organizing center organization / karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / vesicle transport along microtubule / microtubule plus-end binding / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / microtubule associated complex / dynein intermediate chain binding / nuclear migration / dynein complex binding / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic microtubule / 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, 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 regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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: 3.25 Å
AuthorsKendrick, A.A. / Leschziner, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Multiple steps of dynein activation by Lis1 visualized by cryo-EM.
Authors: Agnieszka A Kendrick / Kendrick H V Nguyen / Wen Ma / Eva P Karasmanis / Rommie E Amaro / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role ...Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role in dynein activation. We recently identified a structure of partially autoinhibited dynein bound to Lis1, which suggests an intermediate state in dynein's activation pathway. However, other structural information is needed to fully understand how Lis1 activates dynein. Here, we used cryo-EM and yeast dynein and Lis1 incubated with ATP at different time points to reveal conformations that we propose represent additional intermediate states in dynein's activation pathway. We solved 16 high-resolution structures, including 7 distinct dynein and dynein-Lis1 structures from the same sample. Our data support a model in which Lis1 relieves dynein autoinhibition by increasing its basal ATP hydrolysis rate and promoting conformations compatible with complex assembly and motility. Together, this analysis advances our understanding of dynein activation and the contribution of Lis1 to this process.
History
DepositionSep 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)447,3998
Polymers445,5863
Non-polymers1,8135
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 331525.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DYN1, DHC1, YKR054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): 204508 / S288c / References: UniProt: P36022
#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) / Strain (production host): 204508 / S288c / References: UniProt: P39946
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: yeast dynein in the presence of ATP and PAC1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Buffer solutionpH: 8
Details: 50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28077 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324285
ELECTRON MICROSCOPYf_angle_d0.57232959
ELECTRON MICROSCOPYf_dihedral_angle_d6.1513277
ELECTRON MICROSCOPYf_chiral_restr0.0443786
ELECTRON MICROSCOPYf_plane_restr0.0044134

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