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- PDB-5afu: Cryo-EM structure of dynein tail-dynactin-BICD2N complex -

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Entry
Database: PDB / ID: 5afu
TitleCryo-EM structure of dynein tail-dynactin-BICD2N complex
Components
  • (DYNACTIN) x 11
  • (DYNEIN TAIL) x 4
  • (F-ACTIN-CAPPING PROTEIN SUBUNIT ...) x 3
  • ACTIN, CYTOPLASMIC 1
  • CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1
  • DYNACTIN 6
  • F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II
KeywordsMOTOR PROTEIN / DYNEIN / DYNACTIN / BICD2 / MOTOR / 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 / Neutrophil degranulation / postsynaptic actin cytoskeleton / Tat protein binding / coronary vasculature development / 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 / Recruitment of NuMA to mitotic centrosomes / tight junction / COPI-mediated anterograde transport / aorta development / ventricular septum development / apical junction complex / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / 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 / actin cytoskeleton / lamellipodium / 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 / protein-containing complex / ATP hydrolysis activity / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 7 Propeller / Methylamine Dehydrogenase; Chain H / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin / Dynactin subunit 2 / Dynactin / Dynactin / Dynein tail / F-actin-capping protein subunit alpha-1 / Dynactin subunit 6 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin / Dynactin subunit 2 / Dynactin / Dynactin / Dynein tail / 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: 8.2 Å
AuthorsUrnavicius, L. / Zhang, K. / Diamant, A.G. / Motz, C. / Schlager, 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
DepositionJan 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)884,75143
Polymers880,39933
Non-polymers4,35210
Water00
1


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

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Components

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Protein , 16 types, 27 molecules 123456ABCDEFGIHJKLMNOPQRUVb

#1: Protein DYNEIN TAIL


Mass: 30740.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#2: Protein DYNEIN TAIL


Mass: 30570.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#3: Protein DYNEIN TAIL


Mass: 38900.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: A0A0J9X2A1*PLUS
#4: Protein DYNEIN TAIL


Mass: 23421.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#5: Protein
DYNACTIN


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
#6: Protein ACTIN, CYTOPLASMIC 1 / BETA-ACTIN / ACTIN / CYTOPLASMIC 1 / N-TERMINALLY PROCESSED


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
#7: Protein DYNACTIN


Mass: 42141.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: I3LHK5
#8: 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
#9: 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


Mass: 49974.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#11: Protein DYNACTIN 6


Mass: 52442.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#12: Protein DYNACTIN


Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#13: Protein DYNACTIN


Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#14: Protein DYNACTIN


Mass: 18343.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D0G6S1*PLUS
#15: Protein DYNACTIN


Mass: 18178.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X291*PLUS
#19: Protein DYNACTIN


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

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F-ACTIN-CAPPING PROTEIN SUBUNIT ... , 3 types, 3 molecules YZz

#16: Protein F-ACTIN-CAPPING PROTEIN SUBUNIT BETA / CAPZ BETA


Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#17: Protein F-ACTIN-CAPPING PROTEIN SUBUNIT BETA


Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN
#22: Protein F-ACTIN-CAPPING PROTEIN SUBUNIT BETA / CAPZ BETA


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN

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Protein/peptide , 3 types, 3 molecules acd

#18: Protein/peptide DYNACTIN


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
#20: Protein/peptide DYNACTIN


Mass: 3019.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X299*PLUS
#21: Protein/peptide DYNACTIN


Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X295*PLUS

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Non-polymers , 2 types, 10 molecules

#23: 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
#24: 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

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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: CRYO-EM STRUCTURE OF DYNEIN TAIL-DYNACTIN- BICD2N COMPLEX
Type: COMPLEX
Details: THE PARTICLES WERE SELECTED USING AN AUTOMATIC SELECTION PROGRAM.
Buffer solutionName: 150MM KCL, 25MM HEPES-KOH, 1MM MGCL2, 0.1MM MGATP, 5MM DTT
pH: 7.4
Details: 150MM KCL, 25MM HEPES-KOH, 1MM MGCL2, 0.1MM MGATP, 5MM DTT
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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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: 47000 X / Calibrated magnification: 82353 X / Nominal defocus max: 8000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 14423
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85744 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
RefinementHighest resolution: 8.2 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55678 0 274 0 55952

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