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- PDB-9si3: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome -

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Basic information

Entry
Database: PDB / ID: 9si3
TitleChromosomal Passenger Complex in complex with H3T3ph Nucleosome
Components
  • (DNA (147-MER)) x 2
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • Histone H2A type 1
  • Histone H2B type 1-J
  • Histone H3.2
  • Histone H4
  • Inner centromere protein
KeywordsCELL CYCLE / Nucleosome-binding DNA-binding Stabilising Nucleosome Acidic-patch interaction
Function / homology
Function and homology information


central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis / mitotic spindle midzone assembly / 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 / spindle midzone / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic sister chromatid segregation / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity / chromosome organization / pericentric heterochromatin / protein localization to CENP-A containing chromatin / intercellular bridge / cytoplasmic microtubule / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / tubulin binding / positive regulation of mitotic cell cycle / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / Assembly of the ORC complex at the origin of replication / molecular function activator activity / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / mitotic spindle organization / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / spindle microtubule / chromosome segregation / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / kinetochore / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / small GTPase binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / Metalloprotease DUBs / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / Separation of Sister Chromatids / structural constituent of chromatin / UCH proteinases
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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Baculoviral IAP repeat-containing protein 5 / Histone H2B type 1-J / Histone H2A type 1 / Histone H4 / Histone H3.2 / Borealin / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsGireesh, A. / Abad, M.A. / Sotelo-Parrilla, P. / Jeyaprakash, A.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO J / Year: 2025
Title: Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity.
Authors: Anjitha Gireesh / Maria Alba Abad / Ryu-Suke Nozawa / Paula Sotelo-Parrilla / Léa C Dury / Mariia Likhodeeva / Martin Wear / Christos Spanos / Cristina Cardenal Peralta / Juri Rappsilber / ...Authors: Anjitha Gireesh / Maria Alba Abad / Ryu-Suke Nozawa / Paula Sotelo-Parrilla / Léa C Dury / Mariia Likhodeeva / Martin Wear / Christos Spanos / Cristina Cardenal Peralta / Juri Rappsilber / Karl-Peter Hopfner / Marcus D Wilson / Willem Vanderlinden / Toru Hirota / A Arockia Jeyaprakash /
Abstract: The chromosomal passenger complex (CPC; Borealin-Survivin-INCENP-Aurora B kinase) ensures accurate chromosome segregation by orchestrating sister chromatid cohesion, error correction of kinetochore- ...The chromosomal passenger complex (CPC; Borealin-Survivin-INCENP-Aurora B kinase) ensures accurate chromosome segregation by orchestrating sister chromatid cohesion, error correction of kinetochore-microtubule attachments, and spindle assembly checkpoint signaling. Correct spatiotemporal regulation of CPC is critical for its function. Phosphorylations of histone H3 Thr3 and histone H2A Thr120 and modification-independent nucleosome interactions involving Survivin and Borealin contribute to CPC centromere enrichment. However, how various nucleosome binding elements collectively contribute to CPC centromere enrichment at the mechanistic level, and whether CPC has any non-catalytic role at centromere remain open questions. Combining the high-resolution cryo-EM structure of a CPC-bound H3Thr3ph nucleosome with atomic force microscopy and biochemical and cellular assays, we demonstrate that CPC employs multipartite interactions, which facilitate its engagement with nucleosome acidic patch and the DNA entry-exit site. Perturbing the CPC-nucleosome interaction compromises chromatin protection against MNase digestion in vitro, and centromeric chromatin stability and error-free chromosome segregation in cells. Our work suggests a non-catalytic chromatin-stabilizing role of CPC in maintaining centromeric chromatin features critical for kinetochore function.
History
DepositionAug 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)384,26014
Polymers384,26014
Non-polymers00
Water00
1


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

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Components

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Protein , 7 types, 12 molecules LOAEBFCGDHMN

#1: 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: 31376.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q53HL2
#2: Protein Histone H3.2


Mass: 15303.930 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84233
#3: Protein Histone H4


Mass: 11263.231 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62799
#4: Protein Histone H2A type 1 / H2A.1 / Histone H2A/ptl


Mass: 13990.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H2AC11, H2AFP, HIST1H2AG, H2AC13, H2AFC, HIST1H2AI, H2AC15, H2AFD, HIST1H2AK, H2AC16, H2AFI, HIST1H2AL, H2AC17, H2AFN, HIST1H2AM
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0C0S8
#5: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13804.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P06899
#8: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16414.736 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O15392
#9: Protein Inner centromere protein


Mass: 105620.344 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NQS7

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (147-MER)


Mass: 45644.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#7: DNA chain DNA (147-MER)


Mass: 45105.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome
Type: COMPLEX
Details: Cryo-EM Structure of CPC in complex with H3T3ph Nucleosome
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: .341 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.115 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75653 / Symmetry type: POINT

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