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- PDB-9si9: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (... -

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Basic information

Entry
Database: PDB / ID: 9si9
TitleChromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0)
Components
  • (DNA (147-MER)) x 2
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • H3.4 histone
  • 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 / pericentric heterochromatin / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / chromosome organization / protein localization to CENP-A containing chromatin / intercellular bridge / Replacement of protamines by nucleosomes in the male pronucleus / cytoplasmic microtubule / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / centriole / EML4 and NUDC in mitotic spindle formation / tubulin binding / Inhibition of DNA recombination at telomere / positive regulation of mitotic cell cycle / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / molecular function activator activity / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / chromosome segregation / HDACs deacetylate histones / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / kinetochore / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / small GTPase binding / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Separation of Sister Chromatids / UCH proteinases / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin
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 / 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 / H3.4 histone
Similarity search - Component
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 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: To Be Published
Title: CPC mediated centromeric chromatin protection is essential for error-free chromosome segregation
Authors: Gireesh, A. / Abad, M.A. / Parrilla, P.S. / Jeyaprakash, A.A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (147-MER)
J: DNA (147-MER)
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B type 1-J
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 1-J
L: Borealin
M: Baculoviral IAP repeat-containing protein 5
N: Inner centromere protein
E: H3.4 histone
O: Borealin


Theoretical massNumber of molelcules
Total (without water)384,34014
Polymers384,34014
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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DNA chain , 2 types, 2 molecules IJ

#1: 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)
#2: 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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Protein , 8 types, 12 molecules ABFCGDHLOMNE

#3: Protein Histone H3.2


Mass: 15303.930 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84233
#4: 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
#5: 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
#6: 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
#7: 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
#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
#10: Protein H3.4 histone


Mass: 15383.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: S4RAZ3

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Details

Has ligand of interestY
Has protein modificationY

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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 (Class 0)
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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73078 / Symmetry type: POINT
RefinementHighest resolution: 2.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515331
ELECTRON MICROSCOPYf_angle_d0.61421936
ELECTRON MICROSCOPYf_dihedral_angle_d30.0124378
ELECTRON MICROSCOPYf_chiral_restr0.0372472
ELECTRON MICROSCOPYf_plane_restr0.0041768

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