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- EMDB-17835: Consensus cryo-EM structure of Dynein-Dynactin-JIP3(1-185)-LIS1 -

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Basic information

Entry
Database: EMDB / ID: EMD-17835
TitleConsensus cryo-EM structure of Dynein-Dynactin-JIP3(1-185)-LIS1
Map data
Sample
  • Complex: Composite structure of Dynein-Dynactin-JIP3-LIS1
KeywordsDynein / AAA-Atpase / p150 / LIS1 / MOTOR PROTEIN / Dynactin / JIP3
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSingh K / Lau CK / Manigrasso G / Gassmann R / 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 197-2021European Union
CitationJournal: Science / Year: 2024
Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter /
Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
History
DepositionJul 12, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17835.png

Downloads & links

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Map

FileDownload / File: emd_17835.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 800 pix.
= 847.2 Å		1.06 Å/pix.
x 800 pix.
= 847.2 Å		1.06 Å/pix.
x 800 pix.
= 847.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0013
Minimum - Maximum-0.0021904728 - 0.008674042
Average (Standard dev.)0.0000044882463 (±0.00020678599)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 847.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17835_msk_1.map
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Additional map: Postprocessed map

Fileemd_17835_additional_1.map
AnnotationPostprocessed map
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Half map: #1

Fileemd_17835_half_map_1.map
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Half map: #2

Fileemd_17835_half_map_2.map
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Sample components

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Entire : Composite structure of Dynein-Dynactin-JIP3-LIS1

EntireName: Composite structure of Dynein-Dynactin-JIP3-LIS1
Components
  • Complex: Composite structure of Dynein-Dynactin-JIP3-LIS1

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Supramolecule #1: Composite structure of Dynein-Dynactin-JIP3-LIS1

SupramoleculeName: Composite structure of Dynein-Dynactin-JIP3-LIS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7, #9, #11, #10, #12, #8, #13-#19
Source (natural)Organism: Homo sapiens (human)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 435613
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7z8g


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF Chimera

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