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- EMDB-52832: Helical reconstruction of a D. melanogaster N-clamp-decorated mic... -

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Entry
Database: EMDB / ID: EMD-52832
TitleHelical reconstruction of a D. melanogaster N-clamp-decorated microtubule
Map dataHelical reconstruction of D. melanogaster N-clamp-decorated microtubules
Sample
  • Complex: Microtubule decorated with D. melanogaster N-clamp
    • Complex: Heterotetrameric Augmin TII N-clamp complex
    • Organelle or cellular component: Microtubule
Keywordsaugmin / N-clamp / TII / microtubule / branching / nucleation / HAUS / HAUS augmin-like complex subunit / HAUS6 / HAUS7 / HAUS2 / HAUS8 / Dgt6 / Msd5 / Dgt4 / Msd1 / Drosophila / melanogaster / complex / CH domain / calponin homology domain / CELL CYCLE
Biological speciesDrosophila melanogaster (fruit fly) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWuertz M / Vermeulen BJA / Tonon G / Pfeffer S
Funding support Germany, 12 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Sch Baden-Wuerttemberg Germany
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1503-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)SCHI 295/11-1 Germany
German Research Foundation (DFG)SCHI 295/9-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
Other private Germany
Other private Germany
Other government Germany
CitationJournal: Nat Commun / Year: 2025
Title: Conserved function of the HAUS6 calponin homology domain in anchoring augmin for microtubule branching.
Authors: Martin Würtz / Giulia Tonon / Bram J A Vermeulen / Maja Zezlina / Qi Gao / Annett Neuner / Angelika Seidl / Melanie König / Maximilian Harkenthal / Sebastian Eustermann / Sylvia Erhardt / ...Authors: Martin Würtz / Giulia Tonon / Bram J A Vermeulen / Maja Zezlina / Qi Gao / Annett Neuner / Angelika Seidl / Melanie König / Maximilian Harkenthal / Sebastian Eustermann / Sylvia Erhardt / Fabio Lolicato / Elmar Schiebel / Stefan Pfeffer /
Abstract: Branching microtubule nucleation is a key mechanism for mitotic and meiotic spindle assembly and requires the hetero-octameric augmin complex. Augmin recruits the major microtubule nucleator, the γ- ...Branching microtubule nucleation is a key mechanism for mitotic and meiotic spindle assembly and requires the hetero-octameric augmin complex. Augmin recruits the major microtubule nucleator, the γ-tubulin ring complex, to pre-existing microtubules to direct the formation of new microtubules in a defined orientation. Although recent structural work has provided key insights into the structural organization of augmin, molecular details of its interaction with microtubules remain elusive. Here, we identify the minimal conserved microtubule-binding unit of augmin across species and demonstrate that stable microtubule anchoring is predominantly mediated via the calponin homology (CH) domain in Dgt6/HAUS6. Comparative sequence and functional analyses in vitro and in vivo reveal a highly conserved functional role of the HAUS6 CH domain in microtubule binding. Using cryo-electron microscopy and molecular dynamics simulations in combination with AlphaFold structure predictions, we show that the D. melanogaster Dgt6/HAUS6 CH domain binds microtubules at the inter-protofilament groove between two adjacent β-tubulin subunits and thereby orients augmin on microtubules. Altogether, our findings reveal how augmin binds microtubules to pre-determine the branching angle during microtubule nucleation and facilitate the rapid assembly of complex microtubule networks.
History
DepositionFeb 14, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52832.png

Downloads & links

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Map

FileDownload / File: emd_52832.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of D. melanogaster N-clamp-decorated microtubules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 432 pix.
= 461.808 Å		1.07 Å/pix.
x 432 pix.
= 461.808 Å		1.07 Å/pix.
x 432 pix.
= 461.808 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0157
Minimum - Maximum-0.040068217 - 0.083540894
Average (Standard dev.)0.00011440372 (±0.0035249207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 461.808 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for the helical reconstruction of...

Fileemd_52832_half_map_1.map
AnnotationHalf map 1 for the helical reconstruction of D. melanogaster N-clamp-decorated microtubules
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for the helical reconstruction of...

Fileemd_52832_half_map_2.map
AnnotationHalf map 2 for the helical reconstruction of D. melanogaster N-clamp-decorated 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 : Microtubule decorated with D. melanogaster N-clamp

EntireName: Microtubule decorated with D. melanogaster N-clamp
Components
  • Complex: Microtubule decorated with D. melanogaster N-clamp
    • Complex: Heterotetrameric Augmin TII N-clamp complex
    • Organelle or cellular component: Microtubule

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Supramolecule #1: Microtubule decorated with D. melanogaster N-clamp

SupramoleculeName: Microtubule decorated with D. melanogaster N-clamp / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #2: Heterotetrameric Augmin TII N-clamp complex

SupramoleculeName: Heterotetrameric Augmin TII N-clamp complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #3: Microtubule

SupramoleculeName: Microtubule / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.8
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: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.75 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.74 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102166
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Synthetic reference provided under https://github.com/moores-lab/MiRPv2/tree/main/data/protofilament_sorting_references
Final angle assignmentType: NOT APPLICABLE

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