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- EMDB-55012: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (... -

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Basic information

Entry
Database: EMDB / ID: EMD-55012
TitleChromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy map)
Map data
Sample
  • Complex: Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particle (Double occupancy map)
    • Protein or peptide: Borealin
    • Protein or peptide: Baculoviral IAP repeat-containing protein 5
    • Protein or peptide: Inner centromere protein
    • DNA: Widom 601 DNA (147bp)
    • DNA: Widom 601 DNA (147bp)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
KeywordsCPC / Nucleosome binding protein / Chromosome segregation / Chromatin protection / CELL CYCLE
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGireesh A / Abad MA / Sotelo-Parrilla P / Jeyaprakash AA
Funding supportEuropean Union, 1 items
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
DepositionSep 4, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55012.png

Downloads & links

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Map

FileDownload / File: emd_55012.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.)
0.73 Å/pix.
x 384 pix.
= 279.168 Å		0.73 Å/pix.
x 384 pix.
= 279.168 Å		0.73 Å/pix.
x 384 pix.
= 279.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.39358726 - 0.91138256
Average (Standard dev.)-0.000504693 (±0.031340744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55012_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55012_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particl...

EntireName: Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particle (Double occupancy map)
Components
  • Complex: Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particle (Double occupancy map)
    • Protein or peptide: Borealin
    • Protein or peptide: Baculoviral IAP repeat-containing protein 5
    • Protein or peptide: Inner centromere protein
    • DNA: Widom 601 DNA (147bp)
    • DNA: Widom 601 DNA (147bp)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B

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Supramolecule #1: Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particl...

SupramoleculeName: Chromosomal Passenger Complex with H3T3ph Nucleosome Core Particle (Double occupancy map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 kDa/nm

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Macromolecule #1: Borealin

MacromoleculeName: Borealin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAPRKGSSRV AKTNSLRRRK LASFLKDFDR EVEIRIKQIE SDRQNLLKEV DNLYNIEILR LPKALREMN WLDYFALGGN KQALEEAATA DLDITEINKL TAEAIQTPLK SAKTRKVIQV D EMIVEEEE EEENERKNLQ TARVKRCPPS KKRTQSIQGK GKGKRSSRAN ...String:
MAPRKGSSRV AKTNSLRRRK LASFLKDFDR EVEIRIKQIE SDRQNLLKEV DNLYNIEILR LPKALREMN WLDYFALGGN KQALEEAATA DLDITEINKL TAEAIQTPLK SAKTRKVIQV D EMIVEEEE EEENERKNLQ TARVKRCPPS KKRTQSIQGK GKGKRSSRAN TVTPAVGRLE VS MVKPTPG LTPRFDSRVF KTPGLRTPAA GERIYNISGN GSPLADSKEI FLTVPVGGGE SLR LLASDL QRHSIAQLDP EALGNIKKLS NRLAQICSSI RTHK

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Macromolecule #2: Baculoviral IAP repeat-containing protein 5

MacromoleculeName: Baculoviral IAP repeat-containing protein 5 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MGAPTLPPAW QPFLKDHRIS TFKNWPFLEG CACTPERMAE AGFIHCPTEN EPDLAQCFFC FKELEGWEP DDDPIEEHKK HSSGCAFLSV KKQFEELTLG EFLKLDRERA KNKIAKETNN K KKEFEETA KKVRRAIEQL AAMD

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Macromolecule #3: Inner centromere protein

MacromoleculeName: Inner centromere protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MGTTAPGPIH LLELCDQKLM EFLCNMDNKD LVWLEEIQEE AERMFTREFS KEPELMPKTP SQKNRRKKRR ISYVQDENRD PIRRRLSRRK SRSSQLSSRR LRSKDSVEKL ATVVGENGSV LRRVTRAAAA AAAATMALAA PSSPTPESPT MLTKKPEDNH TQCQLVPVVE IGISERQNAE QHVTQLMSTE

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Macromolecule #6: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
AR(TPO)KQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #7: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #8: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGKV TIAQGGVLPN IQAVLLPKKT ESHHKAKGK

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Macromolecule #9: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVTK YTSAK

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Macromolecule #4: Widom 601 DNA (147bp)

MacromoleculeName: Widom 601 DNA (147bp) / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ACAGGATGTA TATATGTGA C ACGTGCCT GG AGACTAG GGA GTAATC CCCT TGGCG GTTAA AACG CGGGGG ACA GCGCGTA CG TGCGTTTA A GCGGTGCTA GAGCTGTCTA CGACCAATT G AGCGGCCT CG GCACCGG GAT TCTCCA G

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Macromolecule #5: Widom 601 DNA (147bp)

MacromoleculeName: Widom 601 DNA (147bp) / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CTGGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC ACATATATAC ATCCTGT

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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

Concentration115 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28398
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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