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- EMDB-54578: Multibody refinement cryo-EM density map of the apex of the Sacch... -

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Basic information

Entry
Database: EMDB / ID: EMD-54578
TitleMultibody refinement cryo-EM density map of the apex of the Saccharomyces cerevisiae KMN junction complex
Map dataRaw map output by Refine3D. Note not resampled to composite map to preserve high resolution information.
Sample
  • Complex: Saccharomyces cerevisiae outer kinetochore KMN junction complex
    • Complex: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Ndc80c
KeywordsKinetochore / chromosome segregation / mitosis / cell cycle
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsTurner NN / Barford DB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Cancer Research UKC576/A25675 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
CitationJournal: To Be Published
Title: Assembly and phospho-regulatory mechanisms of the budding yeast outer kinetochore KMN complex
Authors: Turner NN / Zhang Z / Yang J / Muir KW / McLaughlin SH / Morgan T / Barford D
History
DepositionJul 28, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54578.png

Downloads & links

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Map

FileDownload / File: emd_54578.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map output by Refine3D. Note not resampled to composite map to preserve high resolution information.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 192 pix.
= 316.8 Å		1.65 Å/pix.
x 192 pix.
= 316.8 Å		1.65 Å/pix.
x 192 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.02073923 - 0.11146124
Average (Standard dev.)0.00021404066 (±0.0026085705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_54578_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Resampled post-processed map used for composite map generation...

Fileemd_54578_additional_2.map
AnnotationResampled post-processed map used for composite map generation and model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw half map output by Refine3D. Note not...

Fileemd_54578_half_map_1.map
AnnotationRaw half map output by Refine3D. Note not resampled to composite map to preserve high resolution information.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw half map output by Refine3D. Note not...

Fileemd_54578_half_map_2.map
AnnotationRaw half map output by Refine3D. Note not resampled to composite map to preserve high resolution information.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae outer kinetochore KMN junction complex

EntireName: Saccharomyces cerevisiae outer kinetochore KMN junction complex
Components
  • Complex: Saccharomyces cerevisiae outer kinetochore KMN junction complex
    • Complex: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
    • Complex: Saccharomyces cerevisiae outer kinetochore Ndc80c

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Supramolecule #1: Saccharomyces cerevisiae outer kinetochore KMN junction complex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore KMN junction complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession ...Details: Imaged sample also contained Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C-terminal HRV-3C protease cleavage site and twin-strep-tag II affinity tag.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c / Location in cell: Nucleus
Molecular weightTheoretical: 187.080 kDa/nm

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Supramolecule #2: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #5, #8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

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Supramolecule #3: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Details: N-terminal truncation of Knl1(Spc105) residues 1-444
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

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Supramolecule #4: Saccharomyces cerevisiae outer kinetochore Ndc80c

SupramoleculeName: Saccharomyces cerevisiae outer kinetochore Ndc80c / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Details: Also contains Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C- ...Details: Also contains Saccharomyces cerevisiae kinetochore protein NDC80 (UniProtKB accession P40460), and Saccharomyces cerevisiae kinetochore protein NUF2 (UniProtKB accession P33895) with a C-terminal HRV-3C protease cleavage site and twin-strep-tag II affinity tag that were present in the imaged sample.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 288c

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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: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium chlorideNaCl
1.0 mMTCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 26390 / Average exposure time: 1.75 sec. / 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: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2592458
Details: Selected using Topaz particle picker trained on manually picked micrographs
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Details: Blush regularization used / Number images used: 113688
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final 3D classificationNumber classes: 4 / Avg.num./class: 28422 / Software - Name: RELION (ver. 5)
Details: Focussed classification using Blush regularization.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4477

chain_id: 24, residue_range: 143-213, source_name: AlphaFold, initial_model_type: in silico model

0014

chain_id: 25, residue_range: 124-221, source_name: AlphaFold, initial_model_type: in silico model

3148

chain_id: Kl, residue_range: 719-917, source_name: AlphaFold, initial_model_type: in silico model

4431

chain_id: Zw, residue_range: 280-368, source_name: AlphaFold, initial_model_type: in silico model

9731

chain_id: Mt, residue_range: 132-289, source_name: AlphaFold, initial_model_type: in silico model

7149

chain_id: Nn, residue_range: 139-201, source_name: AlphaFold, initial_model_type: in silico model

2143

chain_id: Ns, residue_range: 143-216, source_name: AlphaFold, initial_model_type: in silico model

0568

chain_id: Ds, residue_range: 483-576, source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: UCSF ChimeraX
DetailsFlexible fitting using Isolde, real-space refinement using Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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