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- EMDB-2855: CryoEM structure of dynactin complex with p150-glued projection -

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Basic information

Entry
Database: EMDB / ID: EMD-2855
TitleCryoEM structure of dynactin complex with p150-glued projection
Map dataCryoEM reconstruction of dynactin complex with clear extra density of p150-glued projection at 8.6 angstrom resolution.
Sample
  • Sample: Dynactin complex from pig brain
  • Protein or peptide: Actin related protein 1
  • Protein or peptide: Actin related protein 11
  • Protein or peptide: beta-actin
  • Protein or peptide: Dynactin subunit 1
  • Protein or peptide: Dynactin subunit 2
  • Protein or peptide: Dynactin subunit 3
  • Protein or peptide: Actin capping protein
  • Protein or peptide: Dynactin subunit 4
  • Protein or peptide: Dynactin subunit 5
  • Protein or peptide: Dynactin subunit 6
Keywordsdynactin / dynein co-factor / actin-like filament / cellular cargo transport
Function / homology
Function and homology information


centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / 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 / microtubule anchoring at centrosome / Recruitment of mitotic centrosome proteins and complexes ...centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / 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 / microtubule anchoring at centrosome / Recruitment of mitotic centrosome proteins and complexes / ventral spinal cord development / retromer complex / microtubule plus-end / nuclear membrane disassembly / positive regulation of microtubule nucleation / melanosome transport / non-motile cilium assembly / dynein complex / retrograde transport, endosome to Golgi / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule associated complex / COPI-mediated anterograde transport / neuromuscular process / nuclear migration / neuromuscular junction development / cell leading edge / motor behavior / establishment of mitotic spindle orientation / intercellular bridge / neuron projection maintenance / centriole / regulation of mitotic spindle organization / neuron cellular homeostasis / kinetochore / spindle pole / mitotic spindle / nuclear envelope / cell cortex / microtubule binding / ciliary basal body / axon / cell division / neuronal cell body / centrosome / protein kinase binding / cytosol
Similarity search - Function
Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY
Similarity search - Domain/homology
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsZhang K / Urnavicius L / 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 21, 2015-
Header (metadata) releaseMar 4, 2015-
Map releaseMar 4, 2015-
UpdateApr 15, 2015-
Current statusApr 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.088
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.088
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5adx
  • Surface level: 0.088
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2855.png

Downloads & links

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Map

FileDownload / File: emd_2855.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of dynactin complex with clear extra density of p150-glued projection at 8.6 angstrom resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 360 pix.
= 612. Å		1.7 Å/pix.
x 360 pix.
= 612. Å		1.7 Å/pix.
x 360 pix.
= 612. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.088 / Movie #1: 0.088
Minimum - Maximum-0.23348068 - 0.4795756
Average (Standard dev.)0.00077767 (±0.01186519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 612.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z612.000612.000612.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.2330.4800.001

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Supplemental data

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Sample components

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Entire : Dynactin complex from pig brain

EntireName: Dynactin complex from pig brain
Components
  • Sample: Dynactin complex from pig brain
  • Protein or peptide: Actin related protein 1
  • Protein or peptide: Actin related protein 11
  • Protein or peptide: beta-actin
  • Protein or peptide: Dynactin subunit 1
  • Protein or peptide: Dynactin subunit 2
  • Protein or peptide: Dynactin subunit 3
  • Protein or peptide: Actin capping protein
  • Protein or peptide: Dynactin subunit 4
  • Protein or peptide: Dynactin subunit 5
  • Protein or peptide: Dynactin subunit 6

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Supramolecule #1000: Dynactin complex from pig brain

SupramoleculeName: Dynactin complex from pig brain / type: sample / ID: 1000
Details: he sample was stored in -80 degrees Celcius freezer before being loaded onto the grid.
Oligomeric state: One dynactin complex / Number unique components: 10
Molecular weightExperimental: 1.06 MDa / Theoretical: 1.06 MDa / Method: Mass spectrometry

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Macromolecule #1: Actin related protein 1

MacromoleculeName: Actin related protein 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Arp1 / Number of copies: 8 / Oligomeric state: Octamer in actin like filament / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 42.6 KDa / Theoretical: 42.6 KDa

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Macromolecule #2: Actin related protein 11

MacromoleculeName: Actin related protein 11 / type: protein_or_peptide / ID: 2 / Name.synonym: Arp11 / Number of copies: 8 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 46.3 KDa / Theoretical: 46.3 KDa

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Macromolecule #3: beta-actin

MacromoleculeName: beta-actin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 43 KDa / Theoretical: 43 KDa

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Macromolecule #4: Dynactin subunit 1

MacromoleculeName: Dynactin subunit 1 / type: protein_or_peptide / ID: 4 / Name.synonym: DCTN1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 150 KDa / Theoretical: 150 KDa

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Macromolecule #5: Dynactin subunit 2

MacromoleculeName: Dynactin subunit 2 / type: protein_or_peptide / ID: 5 / Name.synonym: DCTN2 / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa

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Macromolecule #6: Dynactin subunit 3

MacromoleculeName: Dynactin subunit 3 / type: protein_or_peptide / ID: 6 / Name.synonym: DCTN3 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 22 KDa / Theoretical: 22 KDa

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Macromolecule #7: Actin capping protein

MacromoleculeName: Actin capping protein / type: protein_or_peptide / ID: 7 / Name.synonym: CapZ / Number of copies: 2 / Oligomeric state: Heterodimer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 33 KDa / Theoretical: 33 KDa

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Macromolecule #8: Dynactin subunit 4

MacromoleculeName: Dynactin subunit 4 / type: protein_or_peptide / ID: 8 / Name.synonym: DCTN4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 62 KDa / Theoretical: 62 KDa

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Macromolecule #9: Dynactin subunit 5

MacromoleculeName: Dynactin subunit 5 / type: protein_or_peptide / ID: 9 / Name.synonym: DCTN5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa

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Macromolecule #10: Dynactin subunit 6

MacromoleculeName: Dynactin subunit 6 / type: protein_or_peptide / ID: 10 / Name.synonym: DCTN6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: Cytoplasm
Molecular weightExperimental: 27 KDa / Theoretical: 27 KDa

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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

Concentration0.07 mg/mL
BufferpH: 6.5
Details: 50mM KCl, 25mM KH2PO4-K2HPO4, 5mM DDT, 1mM MgCl2, 0.1 mM ATP
GridDetails: R2/2 400 square mesh copper grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 105 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times nominal magnification
Legacy - Electron beam tilt params: 0
DateApr 4, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4483 / Average electron dose: 51 e/Å2 / Details: 51 frames per movie / Bits/pixel: 32
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81495 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 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 a GPU accelerated automatic program Gautomatch. The CTF parameter were determined and refined using a GPU accelerated program Gctf
CTF correctionDetails: Each particle by Gctf
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 12870

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