6C0W

Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.7554/eLife.33442
  • Primary Citation of Related Structures:  

  • 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 segregat ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein A
A, E
140Homo sapiensGene Names: CENPA
Find proteins for P49450 (Homo sapiens)
Go to Gene View: CENPA
Go to UniProtKB:  P49450
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Homo sapiensGene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
130Homo sapiensGene Names: HIST1H2AC (H2AFL)
Find proteins for Q93077 (Homo sapiens)
Go to Gene View: HIST1H2AC
Go to UniProtKB:  Q93077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
126Homo sapiensGene Names: HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI (H2BFL, H2BFH, H2BFG, H2BFA, H2BFK)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Centromere protein N
K
295Homo sapiensGene Names: CENPN (C16orf60, ICEN32)
Find proteins for Q96H22 (Homo sapiens)
Go to Gene View: CENPN
Go to UniProtKB:  Q96H22
Entity ID: 5
MoleculeChainsLengthOrganism
147 mer DNAI147Escherichia coli str. 'clone D i2'
Entity ID: 6
MoleculeChainsLengthOrganism
147 mer DNAJ147Escherichia coli str. 'clone D i2'
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM067777
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release