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- EMDB-11314: The shoulder domain of dynactin with underlying Arp1 filament subnits -

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Basic information

Entry
Database: EMDB / ID: EMD-11314
TitleThe shoulder domain of dynactin with underlying Arp1 filament subnits
Map dataMap is aligned using EMDA to EMD-11313.
Sample
  • Complex: Dynactin complex
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLau CK / Lacey SE / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT210711 United Kingdom
CitationJournal: EMBO J / Year: 2021
Title: Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end.
Authors: Clinton K Lau / Francis J O'Reilly / Balaji Santhanam / Samuel E Lacey / Juri Rappsilber / Andrew P Carter /
Abstract: Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled- ...Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.
History
DepositionJul 6, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11314.png

Downloads & links

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Map

FileDownload / File: emd_11314.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap is aligned using EMDA to EMD-11313.
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 AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.31642118 - 0.52059084
Average (Standard dev.)0.00011436405 (±0.0056390595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.3160.5210.000

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Supplemental data

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Mask #1

Fileemd_11314_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Same map as main map, but before fitting using EMDA

Fileemd_11314_additional_1.map
AnnotationSame map as main map, but before fitting using EMDA
Projections & Slices
AxesZYX

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Additional map: Same map as main map, filtered to 6 Angstrom

Fileemd_11314_additional_2.map
AnnotationSame map as main map, filtered to 6 Angstrom
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Mask aligned on map before fitting

Fileemd_11314_additional_3.map
AnnotationMask aligned on map before fitting
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11314_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11314_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Dynactin complex

EntireName: Dynactin complex
Components
  • Complex: Dynactin complex

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Supramolecule #1: Dynactin complex

SupramoleculeName: Dynactin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 1 MDa

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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 #1

Preparation ID1
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Sample preparation #2

Preparation ID2
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Sample preparation #3

Preparation ID3
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Sample preparation #4

Preparation ID4
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Sample preparation #5

Preparation ID5
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 1 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 3 / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~~~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 4 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
DetailsAll 4 image detectors used for reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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