[English] 日本語
Yorodumi
- PDB-8rup: Chromosome Passenger Complex (CPC) localization module in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rup
TitleChromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Components
  • (DNA (147-MER)) x 2
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3
  • Histone H3.2
  • Histone H4
  • Inner centromere protein
KeywordsCELL CYCLE / CPC / nucleosome / chromosome segregation / histone modification / cryoEM
Function / homology
Function and homology information


central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of exit from mitosis / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / lateral element / chromosome passenger complex / protein-containing complex localization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cobalt ion binding / mitotic metaphase chromosome alignment / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic cytokinesis / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / chromosome, centromeric region / cysteine-type endopeptidase inhibitor activity / mitotic spindle assembly / chromosome organization / spindle midzone / pericentric heterochromatin / intercellular bridge / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / tubulin binding / positive regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / molecular function activator activity / mitotic spindle organization / spindle microtubule / chromosome segregation / sensory perception of sound / RHO GTPases Activate Formins / small GTPase binding / kinetochore / spindle / G2/M transition of mitotic cell cycle / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / midbody / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / nuclear body / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / enzyme binding / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / : ...Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / : / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Baculoviral IAP repeat-containing protein 5 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Borealin / Inner centromere protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsRuza, R.R. / Barr, F.A.
Funding support United Kingdom, 1items
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, R.R. / Chung, C.W. / Gold, D.B. / Serena, M. / Roberts, E. / Gruneberg, U. / Barr, F.A.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (147-MER)
J: DNA (147-MER)
K: Baculoviral IAP repeat-containing protein 5
L: Borealin
M: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,53314
Polymers238,46713
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 8 types, 11 molecules ABFCGDHEKLM

#1: Protein Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02281
#5: Protein Histone H3


Mass: 15383.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Gene: LOC121398065, LOC108703785, LOC121398067, XELAEV_18002543mg
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A310TTQ1
#8: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16568.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15392
#9: Protein Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 9138.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53HL2
#10: Protein Inner centromere protein


Mass: 9783.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NQS7

-
DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (147-MER)


Mass: 47128.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#7: DNA chain DNA (147-MER)


Mass: 46709.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 1 types, 1 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Human CPC localisation module in complex with Xenopus H3.T3p-nucleosomeCOMPLEXH3 phosphorylated using purified human Haspin kinase domain (residues 465-798)#1-#100MULTIPLE SOURCES
2H3.T3p-nucleosomeCOMPLEXH3 phosphorylated using purified human Haspin kinase domain (residues 465-798).#1-#51RECOMBINANT
3Chromosome Passenger Complex localisation moduleCOMPLEX#8-#101RECOMBINANT
4DNACOMPLEX#6-#71RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.237 MDaNO
210.202 MDaNO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Xenopus laevis (African clawed frog)8355
43Homo sapiens (human)9606
54synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
54Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
Details: 10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris(hydroxymethyl)aminomethane-hydrochloride(HOCH2)3CNH2-CL1
2150 mMSodium chlorideNaCl1
32 mMDithiothreitolC4H10O2S21
40.3 %n-octyl-beta-D-glucosideC14H28O61
SpecimenConc.: 2.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse sample with good particle density
Specimen supportDetails: 15 mA current, using Leica EM ACE200 / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blotting time, -10 force, no wait time.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 58009 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.51 sec. / Electron dose: 43.86 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20239 / Details: Collected in 2x-binned super-resolution mode
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.0particle selectionBlob-based picking followed by template-based picking
4cryoSPARC4.4.0CTF correctionPatch-CTF estimation job used
7UCSF Chimera1.14model fitting
8Coot0.9.8.1model fitting
10PHENIX1.20.1model refinement
13cryoSPARC4.4.0classification
14cryoSPARC4.4.03D reconstruction
15RELION43D reconstruction
Image processingDetails: Movies motion-corrected on-the-fly using SIMPLE (Caesar, et al., 2020)
CTF correctionDetails: 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
Particle selectionNum. of particles selected: 3099937
Details: Blob-based picking, using 110 A expected particle diameter.
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119063
Details: Final reconstruction performed following particle polishing in Relion and subsequent re-import in CryoSPARC. The CPC distal region was then further locally refined and sharpened using ...Details: Final reconstruction performed following particle polishing in Relion and subsequent re-import in CryoSPARC. The CPC distal region was then further locally refined and sharpened using DeepEMhancer. The resolution value given for the raw final reconstruction before local refinement.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 59.74 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
13AFA

3afa

3AFASequence modified to match Xenopus1
26YIH

6yih

6YIH2

+
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