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- EMDB-56086: Ndc80-decorated microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-56086
TitleNdc80-decorated microtubule
Map data
Sample
  • Complex: Ndc80 complex bound to microtubule
Keywordskinetochore / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsVolkov V
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: EMBO J / Year: 2026
Title: Microtubule end stabilisation by cooperative oligomers of Ska and Ndc80 complexes.
Authors: Renjith M Radhakrishnan / Lauren Stokes / Matthew Day / Pim J Huis In 't Veld / Vladimir A Volkov /
Abstract: During mitosis, properly aligned chromosomes stabilise microtubule ends with the help of kinetochores to ensure timely segregation of chromosomes. Microtubule-binding components of the human outer ...During mitosis, properly aligned chromosomes stabilise microtubule ends with the help of kinetochores to ensure timely segregation of chromosomes. Microtubule-binding components of the human outer kinetochore, such as Ndc80 and Ska complexes, are present in multiple copies and together bind several microtubule ends, creating a highly multivalent binding interface. Whereas Ndc80:Ndc80 and Ndc80:microtubule binding is crucial for interface stability, Ndc80 alone in absence of Ska is unable to support stable kinetochore-attachments. Using cryo-electron tomography, we demonstrate that oligomeric Ndc80:Ska assemblies stabilise microtubule ends against shortening by strengthening lateral contacts between tubulin protofilaments at microtubule plus-ends. We further identify a point mutation within the SKA1 microtubule-binding domain that does not affect microtubule-binding of individual Ska molecules, but does abolish Ska:Ska interactions. Finally, we report that oligomerisation of Ska, in a cooperative fashion together with the Ndc80, is necessary to maintain stable microtubule attachments both in vivo and in vitro.
#1: Journal: Biorxiv / Year: 2025
Title: Microtubule end stabilisation by cooperative oligomers of Ska and Ndc80 complexes
Authors: Radhakrishnan RM / Stokes L / Day M / Huis in t Veld PJ / Volkov VA
History
DepositionDec 15, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56086.png

Downloads & links

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Map

FileDownload / File: emd_56086.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
4.22 Å/pix.
x 128 pix.
= 540.16 Å		4.22 Å/pix.
x 128 pix.
= 540.16 Å		4.22 Å/pix.
x 128 pix.
= 540.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.0
Minimum - Maximum-23.003537999999999 - 39.044379999999997
Average (Standard dev.)-0.000000000069376 (±3.6908388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 540.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56086_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_56086_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ndc80 complex bound to microtubule

EntireName: Ndc80 complex bound to microtubule
Components
  • Complex: Ndc80 complex bound to microtubule

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Supramolecule #1: Ndc80 complex bound to microtubule

SupramoleculeName: Ndc80 complex bound to microtubule / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.9
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: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 1285
ExtractionNumber tomograms: 26 / Number images used: 1285 / Software - Name: RELION (ver. 5.0)
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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