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- PDB-8ruq: Borealin N-terminus in complex with H3.T3p-nucleosome -

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Basic information

Entry
Database: PDB / ID: 8ruq
TitleBorealin N-terminus in complex with H3.T3p-nucleosome
Components
  • (DNA (147-MER)) x 2
  • Borealin
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H3.2
  • Histone H4
KeywordsCELL CYCLE / CPC / nucleosome / chromosome segregation / histone modification / cryoEM
Function / homology
Function and homology information


positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / chromosome passenger complex / mitotic metaphase chromosome alignment / mitotic cytokinesis / mitotic sister chromatid segregation ...positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / chromosome passenger complex / mitotic metaphase chromosome alignment / mitotic cytokinesis / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / chromosome organization / spindle midzone / intercellular bridge / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / microtubule cytoskeleton / midbody / protein heterodimerization activity / nucleolus / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / : / 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 / Histone H2B 1.1 / Histone H4 / Histone H3.2 / Borealin / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
unidentified (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (147-MER)
J: DNA (147-MER)
L: Borealin


Theoretical massNumber of molelcules
Total (without water)211,45911
Polymers211,45911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 9 molecules ABFCGDHEL

#1: 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 (E. coli) / 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 (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 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 (E. coli) / 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 (E. coli) / References: UniProt: A0A310TTQ1
#8: 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
Details: Found in a complex with Survivin(1-142) and INCENP(1-80)
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53HL2

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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.) unidentified (others) / Production host: Escherichia coli (E. coli)
#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.) unidentified (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

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)all0RECOMBINANT
2H3.T3p-nucleosomeCOMPLEXH3 phosphorylated using purified human Haspin kinase domain (residues 465-798).#1-#71RECOMBINANT
3Chromosome Passenger Complex localisation module (Borealin N-terminus only)COMPLEX#81RECOMBINANT
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
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562BL21(DE3)
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562BL21(DE3)
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blotting time, -10 force, no wait time.

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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

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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
12cryoSPARC4.4.0classification
13cryoSPARC4.4.03D reconstruction
14PHENIX1.20.1model refinement
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: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1180547 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 66.48 / 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
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412960
ELECTRON MICROSCOPYf_angle_d0.5718779
ELECTRON MICROSCOPYf_dihedral_angle_d31.0923825
ELECTRON MICROSCOPYf_chiral_restr0.0392152
ELECTRON MICROSCOPYf_plane_restr0.0041358

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