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- PDB-8pqw: Cytoplasmic dynein-1 motor domain bound to dynactin-p150glued and LIS1 -

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Basic information

Entry
Database: PDB / ID: 8pqw
TitleCytoplasmic dynein-1 motor domain bound to dynactin-p150glued and LIS1
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • Dynactin subunit 1
  • Platelet-activating factor acetylhydrolase IB subunit beta
KeywordsMOTOR PROTEIN / Dynein / AAA-Atpase / p150 / LIS1
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / sterol sensor activity / cerebral cortex neuron differentiation / centriolar subdistal appendage / corpus callosum morphogenesis / establishment of centrosome localization / centriole-centriole cohesion / platelet activating factor metabolic process ...microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / sterol sensor activity / cerebral cortex neuron differentiation / centriolar subdistal appendage / corpus callosum morphogenesis / establishment of centrosome localization / centriole-centriole cohesion / platelet activating factor metabolic process / positive regulation of neuromuscular junction development / acrosome assembly / platelet activating factor catabolic process / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / layer formation in cerebral cortex / central region of growth cone / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / auditory receptor cell development / microtubule sliding / lysosome to ER cholesterol transport / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / neuroblast proliferation / microtubule organizing center organization / positive regulation of embryonic development / retromer complex / brain morphogenesis / dynein complex / astral microtubule / microtubule plus-end / mitotic nuclear membrane disassembly / cortical microtubule organization / reelin-mediated signaling pathway / positive regulation of microtubule nucleation / positive regulation of dendritic spine morphogenesis / positive regulation of intracellular transport / positive regulation of spindle assembly / germ cell development / regulation of metaphase plate congression / stem cell division / non-motile cilium assembly / neuromuscular process controlling balance / establishment of spindle localization / stereocilium / microtubule plus-end binding / motor behavior / positive regulation of mitotic cell cycle spindle assembly checkpoint / motile cilium / vesicle transport along microtubule / neuron cellular homeostasis / retrograde axonal transport / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / neuromuscular process / P-body assembly / microtubule associated complex / minus-end-directed microtubule motor activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / dynein light intermediate chain binding / cytoplasmic dynein complex / Recruitment of NuMA to mitotic centrosomes / kinesin complex / nuclear migration / microtubule motor activity / COPI-mediated anterograde transport / microtubule-based movement / male germ cell nucleus / intercellular bridge / establishment of mitotic spindle orientation / dynein intermediate chain binding / cell leading edge / transmission of nerve impulse / neuromuscular junction development / dynein complex binding / dynactin binding / cochlea development / positive regulation of axon extension / adult locomotory behavior / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / positive regulation of mitotic cell cycle / phospholipase binding / cholesterol homeostasis / cytoplasmic microtubule organization / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / neuron projection maintenance / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / centriole
Similarity search - Function
: / : / PAC1 LisH domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 ...: / : / PAC1 LisH domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Lissencephaly type-1-like homology motif / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / Dynactin subunit 1 / Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSingh, K. / Lau, C.K. / Manigrasso, G. / Gassmann, R. / Carter, A.P.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Wellcome Trust210711/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 197-2021European Union
CitationJournal: Science / Year: 2024
Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter /
Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1
B: Platelet-activating factor acetylhydrolase IB subunit beta
C: Platelet-activating factor acetylhydrolase IB subunit beta
D: Platelet-activating factor acetylhydrolase IB subunit beta
E: Platelet-activating factor acetylhydrolase IB subunit beta
F: Dynactin subunit 1
G: Dynactin subunit 1
H: Cytoplasmic dynein 1 intermediate chain 2
I: Cytoplasmic dynein 1 intermediate chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,142,64815
Polymers1,140,8109
Non-polymers1,8376
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

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Cytoplasmic dynein 1 ... , 2 types, 3 molecules AHI

#1: Protein Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 533055.125 Da / Num. of mol.: 1 / Mutation: R1567E, K1610E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204
#4: Protein Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68442.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409

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Protein , 2 types, 6 molecules BCDEFG

#2: Protein
Platelet-activating factor acetylhydrolase IB subunit beta / Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF- ...Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF-AH alpha / PAFAH alpha


Mass: 46709.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034
#3: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / p150-glued


Mass: 142015.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2

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Non-polymers , 3 types, 6 molecules

#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: 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

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Details

Has ligand of interestY

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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-1 bound to dynactin p150 and LIS1 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90594 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7Z8G

7z8g


Accession code: 7Z8G / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00432818
ELECTRON MICROSCOPYf_angle_d0.86944444
ELECTRON MICROSCOPYf_dihedral_angle_d6.5214394
ELECTRON MICROSCOPYf_chiral_restr0.0515027
ELECTRON MICROSCOPYf_plane_restr0.0065694

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