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- EMDB-2860: Electron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex -

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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


RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 / transport along microtubule / visual behavior / 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 / WASH complex / Recruitment of mitotic centrosome proteins and complexes / dynein light chain binding / dynein heavy chain binding / ciliary tip / cellular response to cytochalasin B / Intraflagellar transport / positive regulation of intracellular transport / regulation of transepithelial transport / regulation of metaphase plate congression / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / positive regulation of spindle assembly / barbed-end actin filament capping / protein localization to adherens junction / establishment of spindle localization / dense body / Neutrophil degranulation / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / regulation of cell morphogenesis / dynein complex / adherens junction assembly / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule motor activity / MHC class II antigen presentation / tight junction / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / centrosome localization / COPI-mediated anterograde transport / aorta development / ventricular septum development / microtubule-based movement / nuclear migration / 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 intermediate chain binding / 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 / COPI-mediated anterograde transport / cytoplasmic microtubule / stress fiber / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / cytoskeleton organization / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / stress granule assembly / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / axonogenesis
Similarity search - Function
Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein 1 light intermediate chain / Dynein light chain roadblock-type 1/2 / Dynactin subunit 5 / Dynein family light intermediate chain ...Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein 1 light intermediate chain / Dynein light chain roadblock-type 1/2 / Dynactin subunit 5 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 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 / : / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / 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 / 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 / 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

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Structure visualization

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

emd_2860.png

Downloads & links

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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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 432 pix.
= 578.88 Å		1.34 Å/pix.
x 432 pix.
= 578.88 Å		1.34 Å/pix.
x 432 pix.
= 578.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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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

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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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

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