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- EMDB-52172: Dynactin pointed end in complex with NuMA -

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Basic information

Entry
Database: EMDB / ID: EMD-52172
TitleDynactin pointed end in complex with NuMA
Map data
Sample
  • Complex: Dynein-Dynactin-NuMA-LIS1 complex
    • Complex: Dynactin
    • Complex: NuMA
    • Complex: Dynein-A and Dynein-B
Keywordsmotor protein / transport
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.78 Å
Authorsd'Amico EA / Carter AP
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust227434/Z/23/Z United Kingdom
Wellcome Trust210711/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
UK Research and Innovation (UKRI)EP/Y026004/1 United Kingdom
CitationJournal: Nat Chem Biol / Year: 2026
Title: Activation and regulation of the dynein-dynactin-NuMA complex.
Authors: Merve Aslan / Ennio A d'Amico / Nathan H Cho / Aryan Taheri / Juan M Perez-Bertoldi / Yuanchang Zhao / Xinyue Zhong / Madeline Blaauw / Andrew P Carter / Sophie Dumont / Ahmet Yildiz /
Abstract: During cell division, the nuclear mitotic apparatus protein (NuMA) orchestrates the focusing of microtubule minus-ends in spindle poles and cortical force generation on astral microtubules by ...During cell division, the nuclear mitotic apparatus protein (NuMA) orchestrates the focusing of microtubule minus-ends in spindle poles and cortical force generation on astral microtubules by interacting with dynein motors, microtubules and other cellular factors. Here we used in vitro reconstitution, cryo-electron microscopy and live-cell imaging to understand the mechanism and regulation of NuMA. We determined the structure of the processive dynein-dynactin-NuMA complex (DDN) and showed that the NuMA N terminus drives dynein motility in vitro and facilitates dynein-mediated transport in live cells. The C terminus of NuMA directly binds and suppresses the dynamics of the microtubule minus-end. Full-length NuMA is autoinhibited for its interactions with dynein and microtubules, whereas mitotically phosphorylated NuMA activates dynein in vitro and interphase cells. Together with dynein, activated full-length NuMA focuses microtubule minus-ends into aster-like structures. These results provide critical insights into the activation of NuMA and dynein for their mitotic functions.
History
DepositionNov 21, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52172.png

Downloads & links

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Map

FileDownload / File: emd_52172.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 400 pix.
= 720. Å		1.8 Å/pix.
x 400 pix.
= 720. Å		1.8 Å/pix.
x 400 pix.
= 720. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.3895422 - 2.6790383
Average (Standard dev.)0.0067895544 (±0.06927112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 720.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52172_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_52172_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 : Dynein-Dynactin-NuMA-LIS1 complex

EntireName: Dynein-Dynactin-NuMA-LIS1 complex
Components
  • Complex: Dynein-Dynactin-NuMA-LIS1 complex
    • Complex: Dynactin
    • Complex: NuMA
    • Complex: Dynein-A and Dynein-B

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Supramolecule #1: Dynein-Dynactin-NuMA-LIS1 complex

SupramoleculeName: Dynein-Dynactin-NuMA-LIS1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#9, #16, #10-#13, #1, #14-#15

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Supramolecule #2: Dynactin

SupramoleculeName: Dynactin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#9, #16, #10-#12
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: NuMA

SupramoleculeName: NuMA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Dynein-A and Dynein-B

SupramoleculeName: Dynein-A and Dynein-B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #13, #1, #14-#15
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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8092
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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