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- EMDB-19513: Chromosome Passenger Complex (CPC) localization module in complex... -

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Entry
Database: EMDB / ID: EMD-19513
TitleChromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Map dataComposite map of Xenopus H3.T3p-NCP in complex with human CPC localisation module (Survivin-FL, Borealin(1-76), INCENP(1-80)
Sample
  • Complex: Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
    • Complex: H3.T3p-nucleosome
      • Protein or peptide: x 5 types
    • Complex: Chromosome Passenger Complex localisation module
      • Protein or peptide: x 3 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 1 types
KeywordsCPC / nucleosome / cell cycle / chromosome segregation / histone modification / cryoEM
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 / cysteine-type endopeptidase inhibitor activity / chromosome organization / 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 / RHO GTPases Activate Formins / sensory perception of sound / kinetochore / small GTPase binding / G2/M transition of mitotic cell cycle / spindle / Separation of Sister Chromatids / structural constituent of chromatin / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / midbody / Interleukin-4 and Interleukin-13 signaling / microtubule binding / microtubule / nuclear body / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / 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 / cytoplasm / cytosol
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
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 speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 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
DepositionJan 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19513.png

Downloads & links

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Map

FileDownload / File: emd_19513.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of Xenopus H3.T3p-NCP in complex with human CPC localisation module (Survivin-FL, Borealin(1-76), INCENP(1-80)
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: 0.02
Minimum - Maximum-0.00047961914 - 1.9114597
Average (Standard dev.)0.00094991544 (±0.021301549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19513_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Localised refinement focusing on the distal end of...

Fileemd_19513_additional_1.map
AnnotationLocalised refinement focusing on the distal end of the CPC localisation module.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The raw map of Xenopus H3.T3p-NCP in complex...

Fileemd_19513_additional_2.map
AnnotationThe raw map of Xenopus H3.T3p-NCP in complex with human CPC localisation module (Survivin-FL, Borealin(1-76), INCENP(1-80).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H3
    • Complex: Chromosome Passenger Complex localisation module
      • Protein or peptide: Baculoviral IAP repeat-containing protein 5
      • Protein or peptide: Borealin
      • Protein or peptide: Inner centromere protein
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
  • Ligand: ZINC ION

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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

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Supramolecule #2: H3.T3p-nucleosome

SupramoleculeName: H3.T3p-nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Details: H3 phosphorylated using purified human Haspin kinase domain (residues 465-798).
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.38391 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AR(TPO)KQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #8: Baculoviral IAP repeat-containing protein 5

MacromoleculeName: Baculoviral IAP repeat-containing protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.568902 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPMGAPTLPP AWQPFLKDHR ISTFKNWPFL EGCACTPERM AEAGFIHCPT ENEPDLAQCF FCFKELEGWE PDDDPIEEHK KHSSGCAFL SVKKQFEELT LGEFLKLDRE RAKNKIAKET NNKKKEFEET AKKVRRAIEQ LAAMD

UniProtKB: Baculoviral IAP repeat-containing protein 5

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Macromolecule #9: Borealin

MacromoleculeName: Borealin / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.138654 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAPRKGSSRV AKTNSLRRRK LASFLKDFDR EVEIRIKQIE SDRQNLLKEV DNLYNIEILR LPKALREMNW LDYFAL

UniProtKB: Borealin

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Macromolecule #10: Inner centromere protein

MacromoleculeName: Inner centromere protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.783207 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPMGTTAPGP IHLLELCDQK LMEFLCNMDN KDLVWLEEIQ EEAERMFTRE FSKEPELMPK TPSQKNRRKK RRISYVQDEN RD

UniProtKB: Inner centromere protein

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.128023 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DA)(DT)

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Macromolecule #7: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.709762 KDa
SequenceString: (DA)(DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG) ...String:
(DA)(DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT) (DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG) (DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA) (DT)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT)

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA current, using Leica EM ACE200
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

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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

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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: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 4.4.0), RELION (ver. 4.0))
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.
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)

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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
Output model

PDB-8rup:
Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome

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