6EQT | pdb_00006eqt

CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE PROTEIN CENP-N

• PDB DOI: https://doi.org/10.2210/pdb6EQT/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-15 Released: 2018-01-17 
• Deposition Author(s): Pentakota, S., Vetter, I.R., Petrovic, A., Musacchio, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

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

• PubMed: 29280735 
• DOI: https://doi.org/10.7554/eLife.33442
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, United States.
Department of MCDB, University of Colorado at Boulder, Boulder, United States.
Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
Howard Hughes Medical Institute, Maryland, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.06 kDa 
• Atom Count: 3,478 
• Modeled Residue Count: 412 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein N	A, B	219	Homo sapiens	Mutation(s): 1  Gene Names: CENPN, C16orf60, ICEN32, BM-309
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H22 (Homo sapiens) Explore Q96H22  Go to UniProtKB:  Q96H22
PHAROS:  Q96H22 GTEx:  ENSG00000166451

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.3	α = 90
b = 87.3	β = 90
c = 81.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Pentakota, S., Vetter, I.R., Petrovic, A., Musacchio, A.

Revision History  

• 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