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- PDB-8pr4: Dynactin pointed end bound to JIP3 -

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Basic information

Entry
Database: PDB / ID: 8pr4
TitleDynactin pointed end bound to JIP3
Components
  • (Dynactin subunit ...) x 2
  • Arp11
  • C-Jun-amino-terminal kinase-interacting protein 3
  • Dynactin 6
KeywordsMOTOR PROTEIN / Dynein / AAA-Atpase / p150 / LIS1
Function / homology
Function and homology information


retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / JUN kinase binding / Neutrophil degranulation / coronary vasculature development / regulation of JNK cascade / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation ...retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / JUN kinase binding / Neutrophil degranulation / coronary vasculature development / regulation of JNK cascade / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / axon regeneration / COPI-mediated anterograde transport / aorta development / ventricular septum development / axon development / dynein complex binding / kinesin binding / stress fiber / vesicle-mediated transport / axon cytoplasm / sarcomere / mitotic spindle organization / positive regulation of JNK cascade / kinetochore / signaling receptor complex adaptor activity / cell body / growth cone / cytoplasmic vesicle / cell cortex / nuclear membrane / protein stabilization / Golgi membrane / axon / dendrite / centrosome / negative regulation of apoptotic process / perinuclear region of cytoplasm / nucleoplasm / cytoplasm
Similarity search - Function
JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / Dynactin subunit 4 ...JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / Dynactin subunit 4 / Dynactin p62 family / : / Dynactin subunit 6 / Dynactin subunit 5 / Trimeric LpxA-like superfamily / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 4 / Dynactin subunit 6 / Actin-related protein 10 / C-Jun-amino-terminal kinase-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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
J: Arp11
U: Dynactin 6
W: Dynactin subunit 5
Y: Dynactin subunit 4
X: C-Jun-amino-terminal kinase-interacting protein 3
x: C-Jun-amino-terminal kinase-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,68010
Polymers271,9766
Non-polymers7034
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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Protein , 3 types, 4 molecules JUXx

#1: Protein Arp11


Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5
#2: Protein Dynactin 6


Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1
#5: Protein C-Jun-amino-terminal kinase-interacting protein 3 / JIP-3 / JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / Mitogen-activated protein ...JIP-3 / JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / Mitogen-activated protein kinase 8-interacting protein 3


Mass: 65975.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP3, JIP3, KIAA1066 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UPT6

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Dynactin subunit ... , 2 types, 2 molecules WY

#3: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88
#4: Protein Dynactin subunit 4 / Dynactin subunit 4


Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: Dynactin pointed end bound to JIP3 / Type: COMPLEX / Entity ID: #1-#5 / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98623 / 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_d0.00723466
ELECTRON MICROSCOPYf_angle_d1.19931762
ELECTRON MICROSCOPYf_dihedral_angle_d8.2213235
ELECTRON MICROSCOPYf_chiral_restr0.0633560
ELECTRON MICROSCOPYf_plane_restr0.0094077

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