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- PDB-7pb4: Cenp-HIK 3-protein complex -

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Basic information

Entry
Database: PDB / ID: 7pb4
TitleCenp-HIK 3-protein complex
Components
  • Centromere protein H
  • Centromere protein I
  • Centromere protein K
KeywordsCELL CYCLE / inner kinetochore
Function / homology
Function and homology information


kinetochore organization / inner kinetochore / kinetochore binding / sex differentiation / CENP-A containing chromatin assembly / kinetochore assembly / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...kinetochore organization / inner kinetochore / kinetochore binding / sex differentiation / CENP-A containing chromatin assembly / kinetochore assembly / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / chromosome / nuclear body / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Centromere protein H / Centromere protein H, C-terminal / Centromere protein Cenp-K / Centromere protein H (CENP-H) / Centromere-associated protein K / Centromere protein I / Mis6
Similarity search - Domain/homology
Centromere protein I / Centromere protein K / Centromere protein H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsBellini, D. / Yatskevich, S. / Muir, W.K. / Barford, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2022
Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford /
Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
History
DepositionJul 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Centromere protein H
I: Centromere protein I
K: Centromere protein K


Theoretical massNumber of molelcules
Total (without water)44,0563
Polymers44,0563
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-36 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.625, 56.119, 176.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Centromere protein H / / CENP-H / Interphase centromere complex protein 35


Mass: 5726.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPH, ICEN35 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H3R5
#2: Protein Centromere protein I / / CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / ...CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / Interphase centromere complex protein 19 / Leucine-rich primary response protein 1


Mass: 25832.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI, FSHPRH1, ICEN19, LRPR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92674
#3: Protein Centromere protein K / / CENP-K / Interphase centromere complex protein 37 / Protein AF-5alpha / p33


Mass: 12496.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK, ICEN37, FKSG14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BS16

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 8k, 100 mM imidazole pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→53.5 Å / Num. obs: 11771 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.5
Reflection shellResolution: 2.49→2.6 Å / Rmerge(I) obs: 0.7 / Num. unique obs: 11771 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPC

6ypc


Resolution: 2.49→47.37 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 595 5.06 %
Rwork0.222 11175 -
obs0.2252 11770 72.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.83 Å2 / Biso mean: 50.5043 Å2 / Biso min: 15.03 Å2
Refinement stepCycle: final / Resolution: 2.49→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 0 0 2865
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.740.4052600.28711182124231
2.74-3.140.36671120.31012230234259
3.14-3.950.33131980.2423760395898
3.95-47.370.23562250.185740034228100
Refinement TLS params.Method: refined / Origin x: -19.2463 Å / Origin y: -6.7088 Å / Origin z: 21.7924 Å
111213212223313233
T0.0577 Å2-0.0051 Å20.0315 Å2-0.128 Å2-0.0192 Å2--0.1036 Å2
L0.3295 °20.2513 °20.0273 °2-1.1532 °2-0.108 °2--0.498 °2
S-0.0247 Å °0.0218 Å °-0.0154 Å °-0.0774 Å °-0.0377 Å °0.0184 Å °0.0432 Å °0.0872 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH200 - 246
2X-RAY DIFFRACTION1allI63 - 283
3X-RAY DIFFRACTION1allK165 - 269

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