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- PDB-8pr0: Cytoplasmic dynein-A heavy chain bound to dynactin-p150glued and ... -

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Basic information

Entry
Database: PDB / ID: 8pr0
TitleCytoplasmic dynein-A heavy chain bound to dynactin-p150glued and IC-LC tower
Components
  • (Cytoplasmic dynein 1 ...) x 3
  • (Dynein light chain ...) x 2
  • Dynactin subunit 1
KeywordsMOTOR PROTEIN / Dynein / AAA-Atpase / dynactin / p150 / LC8 / TCTEX1
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / sterol sensor activity / secretory vesicle / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes ...intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / sterol sensor activity / secretory vesicle / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / 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 / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / intraciliary retrograde transport / lysosome to ER cholesterol transport / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / negative regulation of phosphorylation / Activation of BIM and translocation to mitochondria / motile cilium assembly / retromer complex / dynein complex / microtubule plus-end / mitotic nuclear membrane disassembly / Intraflagellar transport / positive regulation of microtubule nucleation / positive regulation of intracellular transport / positive regulation of spindle assembly / regulation of metaphase plate congression / non-motile cilium assembly / establishment of spindle localization / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus / motor behavior / positive regulation of mitotic cell cycle spindle assembly checkpoint / 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 / nuclear migration / microtubule motor activity / COPI-mediated anterograde transport / spermatid development / microtubule-based movement / male germ cell nucleus / intercellular bridge / Macroautophagy / establishment of mitotic spindle orientation / dynein intermediate chain binding / cell leading edge / neuromuscular junction development / tertiary granule membrane / ciliary tip / ficolin-1-rich granule membrane / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / cytoplasmic microtubule organization / cholesterol homeostasis / 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 / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / substantia nigra development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / stress granule assembly / enzyme inhibitor activity / mitotic spindle organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of mitotic spindle organization / filopodium / cellular response to nerve growth factor stimulus / RHO GTPases Activate Formins / microtubule cytoskeleton organization / negative regulation of neurogenesis / mitotic spindle / spindle
Similarity search - Function
: / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) ...: / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / 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 / 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
Dynactin subunit 1 / Cytoplasmic dynein 1 light intermediate chain 2 / Dynein light chain 1, cytoplasmic / Dynein light chain Tctex-type 1 / 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: 9.4 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
D: Cytoplasmic dynein 1 intermediate chain 2
C: Cytoplasmic dynein 1 intermediate chain 2
F: Dynein light chain 1, cytoplasmic
E: Dynein light chain 1, cytoplasmic
G: Dynein light chain Tctex-type 1
H: Dynein light chain Tctex-type 1
I: Dynactin subunit 1
J: Dynactin subunit 1
B: Cytoplasmic dynein 1 heavy chain 1
A: Cytoplasmic dynein 1 heavy chain 1
K: Cytoplasmic dynein 1 light intermediate chain 2


Theoretical massNumber of molelcules
Total (without water)1,586,88611
Polymers1,586,88611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytoplasmic dynein 1 ... , 3 types, 5 molecules DCBAK

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


Mass: 533055.125 Da / Num. of mol.: 2 / 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
#6: Protein Cytoplasmic dynein 1 light intermediate chain 2 / Dynein light intermediate chain 2 / cytosolic / LIC-2 / LIC53/55


Mass: 54173.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237

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Dynein light chain ... , 2 types, 4 molecules FEGH

#2: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal ...8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal nitric oxide synthase / PIN


Mass: 10381.899 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63167
#3: Protein Dynein light chain Tctex-type 1 / Protein CW-1 / T-complex testis-specific protein 1 homolog


Mass: 12461.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLT1, TCTEL1, TCTEX-1, TCTEX1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63172

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Protein , 1 types, 2 molecules IJ

#4: 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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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-A heavy chain bound to dynactin p150 and IC-LC tower
Type: COMPLEX / Entity ID: all / 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 software
IDNameVersionCategory
2PHENIX1.20_4459:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42909 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7Z8G

7z8g


Accession code: 7Z8G / Source name: PDB / Type: experimental model

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