[English] 日本語
Yorodumi
- PDB-5afu: Cryo-EM structure of dynein tail-dynactin-BICD2N complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


COPI-independent Golgi-to-ER retrograde traffic / 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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs ...COPI-independent Golgi-to-ER retrograde traffic / 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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / dynactin complex / 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 / F-actin capping protein complex / negative regulation of filopodium assembly / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / coronary vasculature development / barbed-end actin filament capping / RHO GTPases activate IQGAPs / regulation of lamellipodium assembly / RHO GTPases Activate Formins / aorta development / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / ventricular septum development / dynein complex binding / NuA4 histone acetyltransferase complex / axon cytoplasm / axonogenesis / mitotic spindle organization / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / kinetochore / actin filament binding / actin cytoskeleton / cell cortex / actin cytoskeleton organization / nuclear membrane / cytoskeleton / hydrolase activity / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / 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 / 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, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / : / Dynamitin / Dynamitin / Dynactin subunit 6 / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Actin / Actin family / Actin / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 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. / WD domain, G-beta repeat / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2860
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more