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- EMDB-2861: Electron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2861
TitleElectron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex
Map dataReconstruction of dynein tail/dynactin/GFP-BICD2N complex (TDB). A subset of the dataset were processed to obtain a map at a similar resolution to TDB without GFP.
Sample
  • Sample: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N (subset of particles)
  • Protein or peptide: Human cytoplasmic dynein 1 tail
  • Protein or peptide: pig dynactin
  • Protein or peptide: mouse GFP-BICD2N
Keywordsdynein / dynactin / BICD2 / motor / transport
Biological speciesHomo sapiens (human) / Sus scrofa domesticus (domestic pig) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.8 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: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2861.png

Downloads & links

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Map

FileDownload / File: emd_2861.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 (TDB). A subset of the dataset were processed to obtain a map at a similar resolution to TDB without GFP.
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: 0.055 / Movie #1: 0.1
Minimum - Maximum-0.049855 - 0.1969528
Average (Standard dev.)0.00183708 (±0.01177692)
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-0.0500.1970.002

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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 (subset of p...

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

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Supramolecule #1000: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N (subset of p...

SupramoleculeName: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N (subset of particles)
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
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #2: pig dynactin

MacromoleculeName: pig dynactin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig

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Macromolecule #3: mouse GFP-BICD2N

MacromoleculeName: mouse GFP-BICD2N / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / synonym: house mouse

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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
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: 354 / 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: 6.0 µm / Nominal defocus min: 3.3 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: 11.8 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 6445

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