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- PDB-5adx: CryoEM structure of dynactin complex at 4.0 angstrom resolution -

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Entry
Database: PDB / ID: 5adx
TitleCryoEM structure of dynactin complex at 4.0 angstrom resolution
Components
  • (ACTIN RELATED PROTEIN ...) x 2
  • (DYNACTIN SUBUNIT ...) x 11
  • ACTIN, CYTOPLASMIC 1
  • CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1
  • DYNACTIN 5
  • F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II
KeywordsSTRUCTURAL PROTEIN / DYNEIN CO-FACTOR / ACTIN-LIKE FILAMENT / CELLULAR CARGO TRANSPORT
Function / homology
Function and homology information


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 / UCH proteinases / Gap junction degradation ...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 / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / 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 / F-actin capping protein complex / Recruitment of mitotic centrosome proteins and complexes / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / barbed-end actin filament capping / protein localization to adherens junction / dense body / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / Neutrophil degranulation / dynein complex / adherens junction assembly / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / tight junction / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / aorta development / ventricular septum development / apical junction complex / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / dynein complex binding / brush border / kinesin binding / regulation of synaptic vesicle endocytosis / microtubule-based process / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / axon cytoplasm / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / mitotic spindle organization / actin filament / adherens junction / cell motility / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / actin filament binding / nucleosome / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / nuclear membrane / cytoskeleton / regulation of cell cycle / ribonucleoprotein complex / axon / focal adhesion / synapse / centrosome / protein kinase binding / glutamatergic synapse / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / 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, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / 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 / Ribosomal protein S3 C-terminal domain / 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 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Aspartate Aminotransferase, domain 1 / Actin / Actin family / Actin / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Dynactin subunit 5 / Dynactin / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / Dynactin subunit 6 / F-actin-capping protein subunit beta / Alpha-centractin / Actin-related protein 10 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsZhang, K. / Urnavicius, L. / Diamant, A.G. / Motz, C. / Schlage, M.A. / Yu, M. / Patel, N.A. / Robinson, C.V. / Carter, A.P.
CitationJournal: Science / Year: 2015
Title: The structure of the dynactin complex and its interaction with dynein.
Authors: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter /
Abstract: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components.
History
DepositionAug 24, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionDec 30, 2015ID: 5AFT
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Jul 19, 2017Group: Data collection / Category: em_software
Revision 1.3May 8, 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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Assembly

Deposited unit
A: ACTIN RELATED PROTEIN 1
B: ACTIN RELATED PROTEIN 1
C: ACTIN RELATED PROTEIN 1
D: ACTIN RELATED PROTEIN 1
E: ACTIN RELATED PROTEIN 1
F: ACTIN RELATED PROTEIN 1
G: ACTIN RELATED PROTEIN 1
H: ACTIN, CYTOPLASMIC 1
I: ACTIN RELATED PROTEIN 1
J: ACTIN RELATED PROTEIN 11
K: CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1
L: F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II
M: DYNACTIN SUBUNIT 2
N: DYNACTIN SUBUNIT 2
O: DYNACTIN SUBUNIT 3
P: DYNACTIN SUBUNIT 3
Q: DYNACTIN SUBUNIT 2
R: DYNACTIN SUBUNIT 2
U: DYNACTIN 5
V: DYNACTIN SUBUNIT 6
Y: DYNACTIN SUBUNIT 2
Z: DYNACTIN SUBUNIT 2
a: DYNACTIN SUBUNIT 2
b: DYNACTIN SUBUNIT 2
c: DYNACTIN SUBUNIT 2
d: DYNACTIN SUBUNIT 2
z: DYNACTIN SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)805,39127
Polymers805,39127
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ACTIN RELATED PROTEIN ... , 2 types, 9 molecules ABCDEFGIJ

#1: Protein
ACTIN RELATED PROTEIN 1 / CENTRACTIN / ARP1 / ACTIN-RPV / CENTROSOME-ASSOCIATED ACTIN HOMOLOG


Mass: 41959.930 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: F2Z5G5
#3: Protein ACTIN RELATED PROTEIN 11


Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: I3LHK5

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Protein , 4 types, 4 molecules HKLU

#2: Protein ACTIN, CYTOPLASMIC 1 / BETA-ACTIN


Mass: 41193.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: Q6QAQ1
#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: 31777.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0PFK5
#5: Protein F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II / F-ACTIN-CAPPING PROTEIN SUBUNIT BETA / F-ACTIN-CAPPING PROTEIN SUBUNIT BETA ISOFORM 2


Mass: 30509.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D2JYW4
#10: Protein DYNACTIN 5 / UNCHARACTERIZED PROTEIN


Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D0G6S1

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DYNACTIN SUBUNIT ... , 11 types, 14 molecules MNOPQRVYZzabcd

#6: Protein DYNACTIN SUBUNIT 2


Mass: 70144.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#7: Protein DYNACTIN SUBUNIT 2


Mass: 69633.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#8: Protein DYNACTIN SUBUNIT 3


Mass: 7507.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#9: Protein DYNACTIN SUBUNIT 2


Mass: 7762.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#11: Protein DYNACTIN SUBUNIT 6


Mass: 18164.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X291*PLUS
#12: Protein DYNACTIN SUBUNIT 2


Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#13: Protein DYNACTIN SUBUNIT 2


Mass: 35676.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#14: Protein/peptide DYNACTIN SUBUNIT 2


Mass: 5400.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X292*PLUS
#15: Protein DYNACTIN SUBUNIT 2


Mass: 7931.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS
#16: Protein/peptide DYNACTIN SUBUNIT 2


Mass: 3173.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS
#17: Protein/peptide DYNACTIN SUBUNIT 2


Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS

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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 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig) / Tissue: Brain
Buffer solutionName: 50MM KCL, 25MM K2HPO4- KH2PO4, 1MM MGCL2,5MM DTT / pH: 6.5 / Details: 50MM KCL, 25MM K2HPO4- KH2PO4, 1MM MGCL2,5MM DTT
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ENTHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderTemperature: 90 K / Tilt angle max: 0 °
Image recordingElectron dose: 54 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1RELION3D reconstruction
2GctfCTF correction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115044 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49392 0 0 0 49392

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