[English] 日本語
Yorodumi
- EMDB-2860: Electron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2860
TitleElectron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex
Map dataReconstruction of dynein tail/dynactin/GFP-BICD2N complex.
Sample
  • Sample: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N
  • Protein or peptide: Human cytoplasmic dynein 1 tail
  • Protein or peptide: mouse BICD2N
  • Protein or peptide: pig dynactin
Keywordsdynein / dynactin / BICD2 / motor / transport
Function / homology
Function and homology information


COPI-independent Golgi-to-ER retrograde traffic / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 ...COPI-independent Golgi-to-ER retrograde traffic / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 / transport along microtubule / visual behavior / WASH complex / F-actin capping protein complex / positive regulation of intracellular transport / dynein light chain binding / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / ciliary tip / structural constituent of postsynaptic actin cytoskeleton / dense body / Intraflagellar transport / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / coronary vasculature development / minus-end-directed microtubule motor activity / barbed-end actin filament capping / dynein light intermediate chain binding / cytoplasmic dynein complex / regulation of cell morphogenesis / retrograde axonal transport / RHO GTPases activate IQGAPs / regulation of lamellipodium assembly / RHO GTPases Activate Formins / aorta development / nuclear migration / 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 / centrosome localization / microtubule motor activity / dynein intermediate chain binding / dynein complex binding / NuA4 histone acetyltransferase complex / microtubule-based movement / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / stress fiber / Mitotic Prometaphase / cytoplasmic microtubule organization / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / axon cytoplasm / Recruitment of mitotic centrosome proteins and complexes / cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / axonogenesis / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / kinetochore / cilium / Aggrephagy / microtubule cytoskeleton organization
Similarity search - Function
Dynactin subunit 4 / Dynactin p62 family / : / Dynamitin / Dynamitin / Dynactin subunit 6 / Dynein 1 light intermediate chain / Dynactin subunit 5 / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 ...Dynactin subunit 4 / Dynactin p62 family / : / Dynamitin / Dynamitin / Dynactin subunit 6 / Dynein 1 light intermediate chain / Dynactin subunit 5 / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / 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 / : / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / 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 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynactin subunit 5 / Dynactin / Dynactin subunit 2 / Dynactin / Dynactin / Dynein tail / Dynactin subunit 5 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 ...Dynactin subunit 5 / Dynactin / Dynactin subunit 2 / Dynactin / Dynactin / Dynein tail / Dynactin subunit 5 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / F-actin-capping protein subunit beta / Dynactin subunit 2 / Alpha-centractin / Actin-related protein 10 / Cytoplasmic dynein 1 light intermediate chain 2 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Actin, cytoplasmic 1 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Sus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsUrnavicius L / Zhang K / Diamant AG / Motz C / Schlager MA / Yu M / Patel NA / Robinson CV / Carter AP
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, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseApr 15, 2015-
UpdateApr 22, 2015-
Current statusApr 22, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5afu
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6f3a
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zo4
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2860.png

Downloads & links

-
Map

FileDownload / File: emd_2860.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of dynein tail/dynactin/GFP-BICD2N complex.
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy EMDB: 0.08 / Movie #1: 0.11
Minimum - Maximum-0.12046476 - 0.37087074
Average (Standard dev.)0.00135633 (±0.01193472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 578.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z578.880578.880578.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-0.1200.3710.001

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N

EntireName: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N
Components
  • Sample: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N
  • Protein or peptide: Human cytoplasmic dynein 1 tail
  • Protein or peptide: mouse BICD2N
  • Protein or peptide: pig dynactin

-
Supramolecule #1000: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N

SupramoleculeName: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 3
Molecular weightTheoretical: 2.6 MDa

-
Macromolecule #1: Human cytoplasmic dynein 1 tail

MacromoleculeName: Human cytoplasmic dynein 1 tail / type: protein_or_peptide / ID: 1 / Name.synonym: TDB / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human//Mouse / Location in cell: cytoplasm
Molecular weightTheoretical: 2.6 MDa

-
Macromolecule #2: mouse BICD2N

MacromoleculeName: mouse BICD2N / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / synonym: house mouse

-
Macromolecule #3: pig dynactin

MacromoleculeName: pig dynactin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig / Location in cell: cytoplasm

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.075 mg/mL
BufferpH: 7.4
Details: 150mM KCl, 25mM HEPES-KOH, 1mM MgCl2, 0.1mM MgATP, 5mM DTT
GridDetails: Quantifoil R1.2/1.3 400 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 3.5 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification.
DateJul 17, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4259 / Average electron dose: 1 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 82353 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 85744

+
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