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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 / Separation of Sister Chromatids / structural constituent of chromatin / 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 H2A conserved site / Histone H2A signature. / Histone H2B ...Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / : / 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) / 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
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, 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
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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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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