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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


Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / positive regulation of neuromuscular junction development / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / Gap junction degradation ...Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / positive regulation of neuromuscular junction development / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / 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 / centriole-centriole cohesion / ventral spinal cord development / microtubule anchoring at centrosome / WASH complex / F-actin capping protein complex / negative regulation of filopodium assembly / cellular response to cytochalasin B / melanosome transport / cytoskeleton-dependent cytokinesis / regulation of transepithelial transport / retromer complex / nuclear membrane disassembly / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / microtubule plus-end / positive regulation of microtubule nucleation / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / barbed-end actin filament capping / non-motile cilium assembly / adherens junction assembly / coronary vasculature development / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / regulation of cell morphogenesis / RHO GTPases Activate Formins / regulation of lamellipodium assembly / 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 / retrograde transport, endosome to Golgi / tight junction / nuclear migration / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / microtubule associated complex / motor behavior / NuA4 histone acetyltransferase complex / neuromuscular process / regulation of synaptic vesicle endocytosis / ventricular septum development / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / neuromuscular junction development / intercellular bridge / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / nitric-oxide synthase binding / cell leading edge / establishment of mitotic spindle orientation / cleavage furrow / brush border / kinesin binding / calyx of Held / regulation of protein localization to plasma membrane / microtubule-based process / stress fiber / cytoskeleton organization / regulation of mitotic spindle organization / axon cytoplasm / neuron projection maintenance / centriole / axonogenesis / sarcomere / mitotic spindle organization / ciliary basal body / 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 / cell morphogenesis / cytoplasmic ribonucleoprotein granule / mitotic spindle
Similarity search - Function
Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / : / Dynein associated protein / Dynein associated protein / Dynamitin / Dynamitin / Dynactin subunit 6 ...Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / : / Dynein associated protein / Dynein associated protein / Dynamitin / Dynamitin / Dynactin subunit 6 / 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 / 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 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

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Structure visualization

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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
Water0
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 / Adenosine 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 / Adenosine 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 complexDynactin / 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 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
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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