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- PDB-6znl: Cryo-EM structure of the dynactin complex -

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Basic information

Entry
Database: PDB / ID: 6znl
TitleCryo-EM structure of the dynactin complex
Components
  • (Dynactin subunit ...) x 5
  • ARP1 actin related protein 1 homolog A
  • Actin, cytoplasmic 1
  • Arp11
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • Dynactin 6
  • F-actin capping protein beta subunit
KeywordsSTRUCTURAL PROTEIN / Dynactin / Complex / Scaffold / Cytoskeleton
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / RHOF GTPase cycle ...Advanced glycosylation endproduct receptor signaling / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / RHOF GTPase cycle / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBP-mediated host defense / sterol sensor activity / Platelet degranulation / Gap junction degradation / Formation of annular gap junctions / UCH proteinases / dynactin complex / centriolar subdistal appendage / Clathrin-mediated endocytosis / 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 / F-actin capping protein complex / WASH complex / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / lysosome to ER cholesterol transport / ventral spinal cord development / retromer complex / cytoskeleton-dependent cytokinesis / dynein complex / microtubule plus-end / mitotic nuclear membrane disassembly / positive regulation of microtubule nucleation / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / non-motile cilium assembly / barbed-end actin filament capping / dense body / Neutrophil degranulation / Tat protein binding / motor behavior / postsynaptic actin cytoskeleton / apical protein localization / neuron cellular homeostasis / retrograde transport, endosome to Golgi / adherens junction assembly / neuromuscular process / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / microtubule associated complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / nuclear migration / Recruitment of NuMA to mitotic centrosomes / tight junction / COPI-mediated anterograde transport / apical junction complex / intercellular bridge / establishment of mitotic spindle orientation / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / cell leading edge / cortical cytoskeleton / cleavage furrow / establishment or maintenance of cell polarity / neuromuscular junction development / nitric-oxide synthase binding / dynein complex binding / brush border / regulation of synaptic vesicle endocytosis / kinesin binding / regulation of protein localization to plasma membrane / microtubule-based process / positive regulation of double-strand break repair via homologous recombination / axonogenesis / stress fiber / cholesterol homeostasis / axon cytoplasm / neuron projection maintenance / centriole / calyx of Held / cell motility / nitric-oxide synthase regulator activity / mitotic spindle organization / regulation of mitotic spindle organization
Similarity search - Function
Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / Dynamitin / Dynactin subunit 6 / : / Domain of unknown function (DUF8221) / Dynein associated protein ...Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / Dynamitin / Dynactin subunit 6 / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / : / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Trimeric LpxA-like superfamily / 3 Solenoid / 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 / Alpha-centractin / Actin-related protein 10 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: ARP1 actin related protein 1 homolog A
B: ARP1 actin related protein 1 homolog A
C: ARP1 actin related protein 1 homolog A
D: ARP1 actin related protein 1 homolog A
E: ARP1 actin related protein 1 homolog A
F: ARP1 actin related protein 1 homolog A
G: ARP1 actin related protein 1 homolog A
H: Actin, cytoplasmic 1
I: ARP1 actin related protein 1 homolog A
J: Arp11
K: Capping protein (Actin filament) muscle Z-line, alpha 1
L: F-actin capping protein beta subunit
M: Dynactin subunit 2
N: Dynactin subunit 2
O: Dynactin subunit 3
U: Dynactin 6
V: Dynactin subunit 5
Y: Dynactin subunit 4
Z: Dynactin subunit 1
m: Dynactin subunit 2
n: Dynactin subunit 2
o: Dynactin subunit 3
z: Dynactin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,097,74936
Polymers1,093,20023
Non-polymers4,54813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area148840 Å2
ΔGint-1016 kcal/mol
Surface area289920 Å2
MethodPISA

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Components

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Protein , 6 types, 13 molecules ABCDEFGIHJKLU

#1: Protein
ARP1 actin related protein 1 homolog A


Mass: 42670.688 Da / Num. of mol.: 8 / 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
#4: Protein Capping protein (Actin filament) muscle Z-line, alpha 1 / F-actin capping protein alpha 1 subunit / F-actin capping protein subunit alpha 1


Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5
#5: Protein F-actin capping protein beta subunit / F-actin-capping protein subunit beta / F-actin-capping protein subunit beta isoform 1


Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6
#8: 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

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Dynactin subunit ... , 5 types, 10 molecules MNmnOoVYZz

#6: Protein
Dynactin subunit 2


Mass: 44704.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80
#7: Protein Dynactin subunit 3 / Dynactin subunit 3 isoform 1


Mass: 21192.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SEC0
#9: 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
#10: 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
#11: Protein Dynactin subunit 1


Mass: 142547.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2*PLUS

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Non-polymers , 3 types, 13 molecules

#12: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#13: 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
#14: 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 complex / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig)
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 FIELD
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
19REFMACmodel refinement
20PHENIXmodel refinement
Image processingDetails: All 4 image detectors used for reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336972 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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