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- PDB-6znm: The pointed end complex of dynactin bound to BICDR1 -

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Basic information

Entry
Database: PDB / ID: 6znm
TitleThe pointed end complex of dynactin bound to BICDR1
Components
  • (Dynactin subunit ...) x 3
  • ARP1 actin related protein 1 homolog A
  • Actin, cytoplasmic 1
  • Arp11
  • BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1
  • Dynactin 6
KeywordsSTRUCTURAL PROTEIN / Dynactin / Complex / Scaffold / Cytoskeleton
Function / homology
Function and homology information


Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / dynactin complex / Clathrin-mediated endocytosis / cellular response to cytochalasin B / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / vesicle transport along microtubule / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / adherens junction assembly / coronary vasculature development / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / tight junction / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / ventricular septum development / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / nitric-oxide synthase binding / dynactin binding / brush border / kinesin binding / calyx of Held / regulation of protein localization to plasma membrane / microtubule-based process / stress fiber / axon cytoplasm / axonogenesis / sarcomere / mitotic spindle organization / actin filament / cell motility / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / kinetochore / small GTPase binding / neuron projection development / nucleosome / actin cytoskeleton / lamellipodium / cell cortex / nuclear membrane / microtubule / cytoskeleton / regulation of cell cycle / hydrolase activity / ribonucleoprotein complex / axon / focal adhesion / centrosome / glutamatergic synapse / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dynactin subunit 4 / Dynactin p62 family / : / Dynamitin / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Actins signature 1. ...Dynactin subunit 4 / Dynactin p62 family / : / Dynamitin / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 4 / Dynactin subunit 2 / BICD family-like cargo adapter 1 / Dynactin subunit 6 / Alpha-centractin / Actin-related protein 10 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLau, C.K. / Lacey, S.E. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT210711 United Kingdom
CitationJournal: EMBO J / Year: 2021
Title: Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end.
Authors: Clinton K Lau / Francis J O'Reilly / Balaji Santhanam / Samuel E Lacey / Juri Rappsilber / Andrew P Carter /
Abstract: Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled- ...Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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Assembly

Deposited unit
G: ARP1 actin related protein 1 homolog A
H: Actin, cytoplasmic 1
I: ARP1 actin related protein 1 homolog A
J: Arp11
M: Dynactin subunit 2
U: Dynactin 6
V: Dynactin subunit 5
X: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1
Y: Dynactin subunit 4
x: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,68517
Polymers428,70010
Non-polymers1,9857
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration evidence for the entire dynactin complex bound to BICDR1, with dynein.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 7 molecules GIHJUXx

#1: Protein ARP1 actin related protein 1 homolog A


Mass: 42670.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5
#2: Protein Actin, cytoplasmic 1 / / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#3: 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
#5: 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
#7: Protein BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1 / Bicaudal D-related protein 1 / BICDR-1 / Coiled-coil domain-containing protein 64A


Mass: 58422.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9

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Dynactin subunit ... , 3 types, 3 molecules MVY

#4: Protein Dynactin subunit 2 /


Mass: 44704.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80
#6: 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
#8: Protein Dynactin subunit 4 / / Dynactin subunit 4


Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Dynactin subunit 4 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62

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Non-polymers , 3 types, 7 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#11: 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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Dynein-Dynactin-BICDR1 complexCOMPLEXNote that signal for dyneins and part of dynactin and BICDR1 have been removed by signal subtraction#1-#80MULTIPLE SOURCES
2DynactinCOMPLEX#1-#6, #81NATURAL
3BICDR1COMPLEX#71RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Mus musculus (house mouse)10090
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
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 FIELDBright-field microscopy
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
13REFMACmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205611 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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