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- EMDB-15396: Consensus map of dynein-dynactin-BICDR on microtubules -

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Basic information

Entry
Database: EMDB / ID: EMD-15396
TitleConsensus map of dynein-dynactin-BICDR on microtubules
Map dataConsensus map of Dynein-Dynactin-BICDR on microtubules
Sample
  • Complex: Complex of dynein, dynactin, and BICDR1 bound to microtubules
    • Organelle or cellular component: Dynein, cytoplasmic 1
    • Organelle or cellular component: Dynactin
    • Organelle or cellular component: BICDR1
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.33 Å
AuthorsChaaban S / Carter AP
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust210711/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 334-2020European Union
CitationJournal: Nature / Year: 2022
Title: Structure of dynein-dynactin on microtubules shows tandem adaptor binding.
Authors: Sami Chaaban / Andrew P Carter /
Abstract: Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between ...Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour. Different coiled-coil adaptors are linked to different cargos, and some share motifs known to contact sites on dynein and dynactin. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.
History
DepositionJul 17, 2022-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15396.png

Downloads & links

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Map

FileDownload / File: emd_15396.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of Dynein-Dynactin-BICDR on microtubules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.49 Å/pix.
x 384 pix.
= 955.776 Å		2.49 Å/pix.
x 384 pix.
= 955.776 Å		2.49 Å/pix.
x 384 pix.
= 955.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.489 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0132
Minimum - Maximum-0.011637378 - 0.076103345
Average (Standard dev.)1.2641454e-05 (±0.0019732562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 955.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15396_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of Dynein-Dynactin-BICDR on microtubules

Fileemd_15396_half_map_1.map
AnnotationHalf map 1 of Dynein-Dynactin-BICDR on microtubules
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of Dynein-Dynactin-BICDR on microtubules

Fileemd_15396_half_map_2.map
AnnotationHalf map 2 of Dynein-Dynactin-BICDR on microtubules
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of dynein, dynactin, and BICDR1 bound to microtubules

EntireName: Complex of dynein, dynactin, and BICDR1 bound to microtubules
Components
  • Complex: Complex of dynein, dynactin, and BICDR1 bound to microtubules
    • Organelle or cellular component: Dynein, cytoplasmic 1
    • Organelle or cellular component: Dynactin
    • Organelle or cellular component: BICDR1

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Supramolecule #1: Complex of dynein, dynactin, and BICDR1 bound to microtubules

SupramoleculeName: Complex of dynein, dynactin, and BICDR1 bound to microtubules
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 4 MDa

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Supramolecule #2: Dynein, cytoplasmic 1

SupramoleculeName: Dynein, cytoplasmic 1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #13-#16
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.4 MDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Dynactin

SupramoleculeName: Dynactin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 1.1 MDa

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Supramolecule #4: BICDR1

SupramoleculeName: BICDR1 / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #11
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 130 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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

BufferpH: 7.2
Component:
ConcentrationFormulaName
30.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
60.0 mMKClPotassium chloride
5.0 mMMgSO4Magnesium sulfate
1.0 mMEGTA3,12-Bis(carboxymethyl)-6,9-dioxa-3,12-diazatetradecane-1,14-dioic acid
1.0 mMDTTDithiothreitol
3.0 mMAMPPNPAdenylyl-imidodiphosphate
5.0 uMTaxolPaclitaxelPaclitaxel
0.01 %IGEPALOctylphenoxypolyethoxyethanol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: 20 second incubation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 14 / Number real images: 88715 / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2
Details: Images were collected in movie-mode and fractionated into 53 movie frames
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 628033
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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