7PB4 | pdb_00007pb4

Cenp-HIK 3-protein complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.283 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PB4

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 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.

Macromolecule Content 

  • Total Structure Weight: 44.06 kDa 
  • Atom Count: 2,864 
  • Modeled Residue Count: 353 
  • Deposited Residue Count: 381 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein HA [auth H]49Homo sapiensMutation(s): 0 
Gene Names: CENPHICEN35
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R5 (Homo sapiens)
Explore Q9H3R5 
Go to UniProtKB:  Q9H3R5
PHAROS:  Q9H3R5
GTEx:  ENSG00000153044 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3R5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein IB [auth I]227Homo sapiensMutation(s): 0 
Gene Names: CENPIFSHPRH1ICEN19LRPR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92674 (Homo sapiens)
Explore Q92674 
Go to UniProtKB:  Q92674
PHAROS:  Q92674
GTEx:  ENSG00000102384 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92674
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein KC [auth K]105Homo sapiensMutation(s): 0 
Gene Names: CENPKICEN37FKSG14
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BS16 (Homo sapiens)
Explore Q9BS16 
Go to UniProtKB:  Q9BS16
PHAROS:  Q9BS16
GTEx:  ENSG00000123219 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BS16
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.625α = 90
b = 56.119β = 90
c = 176.704γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata 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