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- EMDB-18485: Ndc80c microtubule complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18485
TitleNdc80c microtubule complex
Map data
Sample
  • Complex: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
KeywordsKinetochore / microtubule / error correction / chromosome segregation / CELL CYCLE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsMuir KW / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
Citation
Journal: Science / Year: 2023
Title: Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules.
Authors: Kyle W Muir / Christopher Batters / Tom Dendooven / Jing Yang / Ziguo Zhang / Alister Burt / David Barford /
Abstract: Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until ...Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
#1: Journal: To Be Published
Title: Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction
Authors: Muir KW / Batters C / Dendooven T / Yang J / Zhang Z / Burt A / Barford D
History
DepositionSep 19, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18485.png

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Map

FileDownload / File: emd_18485.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.008780971 - 0.026771812
Average (Standard dev.)0.00031163316 (±0.0022944433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 572.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18485_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18485_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf...

EntireName: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
Components
  • Complex: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils

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Supramolecule #1: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf...

SupramoleculeName: Outer kinetochore Dam1 protomer monomer with staple and Ndc80-Nuf2 coiled-coils
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 673772.36 MDa

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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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: cryoSPARC (ver. 3.3.2), RELION (ver. 4.0-dev))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110704

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 540.98

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