7PB8

Crystal structure of the CENP-OPQUR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.

Yatskevich, S.Muir, K.W.Bellini, D.Zhang, Z.Yang, J.Tischer, T.Predin, M.Dendooven, T.McLaughlin, S.H.Barford, D.

(2022) Science 376: 844-852

  • DOI: https://doi.org/10.1126/science.abn3810
  • Primary Citation of Related Structures:  
    7PB4, 7PB8, 7PII, 7PKN, 7R5R, 7R5S, 7R5V, 7YWX, 7YYH

  • PubMed Abstract: 

    Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A Nuc ) 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 Nuc reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A Nuc , 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein OA [auth O]300Homo sapiensMutation(s): 0 
Gene Names: CENPOICEN36MCM21R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BU64 (Homo sapiens)
Go to UniProtKB:  Q9BU64
PHAROS:  Q9BU64
GTEx:  ENSG00000138092 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein QB [auth Q]137Homo sapiensMutation(s): 0 
Gene Names: CENPQC6orf139
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2Z9 (Homo sapiens)
Go to UniProtKB:  Q7L2Z9
PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein UC [auth U]418Homo sapiensMutation(s): 0 
Gene Names: CENPUICEN24KLIP1MLF1IPPBIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q71F23 (Homo sapiens)
Go to UniProtKB:  Q71F23
PHAROS:  Q71F23
GTEx:  ENSG00000151725 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein PD [auth P]294Homo sapiensMutation(s): 0 
Gene Names: CENPP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IPU0 (Homo sapiens)
Go to UniProtKB:  Q6IPU0
PHAROS:  Q6IPU0
GTEx:  ENSG00000188312 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein RE [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BPCENPRNRIF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13352 (Homo sapiens)
Go to UniProtKB:  Q13352
PHAROS:  Q13352
GTEx:  ENSG00000142856 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.614α = 90
b = 51.299β = 117.49
c = 109.999γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description