[English] 日本語
Yorodumi
- EMDB-19685: Chromosome Passenger Complex (CPC) localization module in complex... -

+
Open data


ID or keywords:

Loading...

-
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
Citation
Journal: EMBO Rep / Year: 2025
Title: A pivot-tether model for nucleosome recognition by the chromosomal passenger complex.
Authors: Reinis R Ruza / Chyi Wei Chung / Danny B H Gold / Michela Serena / Emile Roberts / Ulrike Gruneberg / Francis A Barr /
Abstract: Spatial restriction of Aurora B to T3-phosphorylated histone H3 (H3pT3) nucleosomes adjacent to centromeres during prometaphase and metaphase enables it to phosphorylate proteins necessary for ...Spatial restriction of Aurora B to T3-phosphorylated histone H3 (H3pT3) nucleosomes adjacent to centromeres during prometaphase and metaphase enables it to phosphorylate proteins necessary for spindle assembly checkpoint signalling and biorientation of chromosomes on the mitotic spindle. Aurora B binding to H3pT3-nucleosomes requires a multivalent targeting module, the chromosomal passenger complex (CPC), consisting of survivin, borealin, and INCENP. To shed light on how these components mediate CPC localisation during prometaphase and metaphase, we determined the structure of the CPC targeting module in complex with haspin-phosphorylated H3pT3-nucleosomes by cryo-electron microscopy. This structure shows how the N-terminus of borealin and the survivin BIR domain act as pivot and flexible tethering points, respectively, to increase CPC affinity for H3pT3 nucleosomes without limiting it to a specific orientation. We demonstrate that this flexible, yet constrained pivot-tether arrangement is important for the control of spindle assembly checkpoint signalling by Aurora B.
#1: Journal: 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-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19685.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_19685_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19685_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Software - details: Patch-CTF estimation job used
Details: CTF amplitude correction first performed following movie motion correction, and CTF parameters were later refined during the refinement of the final reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more