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- EMDB-19685: Chromosome Passenger Complex (CPC) localization module in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-19685
TitleChromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome - raw concensus map
Map data
Sample
  • Complex: Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
    • Complex: H3.T3p-nucleosome
    • Complex: Chromosome Passenger Complex localisation module
KeywordsCPC / nucleosome / cell cycle / chromosome segregation / histone modification / cryoEM
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRuza RR / Barr FA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UKC20079/A24743 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: A pivot-tether model for nucleosome recognition by the chromosomal passenger complex
Authors: Ruza RR / Chung CW / Gold DB / Serena M / Roberts E / Gruneberg U / Barr FA
History
DepositionFeb 19, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19685.png

Downloads & links

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Map

FileDownload / File: emd_19685.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.33240375 - 0.981741
Average (Standard dev.)0.0014026157 (±0.021020362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19685_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_19685_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 : Human CPC localisation module in complex with Xenopus H3.T3p-nucl...

EntireName: Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
Components
  • Complex: Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
    • Complex: H3.T3p-nucleosome
    • Complex: Chromosome Passenger Complex localisation module

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Supramolecule #1: Human CPC localisation module in complex with Xenopus H3.T3p-nucl...

SupramoleculeName: Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Details: H3 phosphorylated using purified human Haspin kinase domain (residues 465-798)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 202 KDa

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Supramolecule #2: H3.T3p-nucleosome

SupramoleculeName: H3.T3p-nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7
Details: H3 phosphorylated using purified human Haspin kinase domain (residues 465-798).
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: Chromosome Passenger Complex localisation module

SupramoleculeName: Chromosome Passenger Complex localisation module / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#10
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

Concentration2.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mM(HOCH2)3CNH2-CLTris(hydroxymethyl)aminomethane-hydrochloride
150.0 mMNaClSodium chloride
2.0 mMC4H10O2S2Dithiothreitol
0.3 %C14H28O6n-octyl-beta-D-glucoside

Details: 10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 s blotting time, -10 force, no wait time..
DetailsMonodisperse sample with good particle density

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20239 / Average exposure time: 2.51 sec. / Average electron dose: 43.86 e/Å2 / Details: Collected in 2x-binned super-resolution mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 58009
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMovies motion-corrected on-the-fly using SIMPLE (Caesar, et al., 2020)
Particle selectionNumber selected: 3099937
Details: Blob-based picking, using 110 A expected particle diameter.
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 4.4.0), RELION (ver. 4.0)) / Number images used: 119063
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 83358 / Software - Name: cryoSPARC (ver. 4.4.0)
Details: Performed using a heterogenous refinement job with 2 classes.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

3afa

source_name: PDB, initial_model_type: experimental modelSequence modified to match Xenopus

6yih

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 59.74 / Target criteria: Cross-correlation coefficient

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