6EQT

CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE PROTEIN CENP-N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Decoding the centromeric nucleosome through CENP-N.

Pentakota, S.Zhou, K.Smith, C.Maffini, S.Petrovic, A.Morgan, G.P.Weir, J.R.Vetter, I.R.Musacchio, A.Luger, K.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.33442
  • Primary Citation of Related Structures:  
    6C0W, 6EQT

  • PubMed Abstract: 

    Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A. It also engages in extensive interactions with a 15-base pair segment of the distorted nucleosomal DNA double helix, in a position predicted to exclude chromatin remodelling enzymes. Besides CENP-A, stable centromere recruitment of CENP-N requires a coincident interaction with a newly identified binding motif on nucleosome-bound CENP-C. Collectively, our studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly.


  • Organizational Affiliation

    Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein N
A, B
219Homo sapiensMutation(s): 1 
Gene Names: CENPNC16orf60ICEN32BM-309
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H22 (Homo sapiens)
Explore Q96H22 
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96H22
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.3α = 90
b = 87.3β = 90
c = 81.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Refinement description
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references