7U47

CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

CENP-N promotes the compaction of centromeric chromatin.

Zhou, K.Gebala, M.Woods, D.Sundararajan, K.Edwards, G.Krzizike, D.Wereszczynski, J.Straight, A.F.Luger, K.

(2022) Nat Struct Mol Biol 29: 403-413

  • DOI: 10.1038/s41594-022-00758-y
  • Primary Citation of Related Structures:  
    7U46, 7U47, 7U4D

  • PubMed Abstract: 
  • The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown ...

    The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA. Karolin.Luger@colorado.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AA, E, L, P140Homo sapiensMutation(s): 0 
Gene Names: CENPA
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Find proteins for P49450 (Homo sapiens)
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PHAROS:  P49450
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UniProt GroupP49450
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, M, Q103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G, N, R130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ACH2AFLH2AC6
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Find proteins for Q93077 (Homo sapiens)
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PHAROS:  Q93077
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UniProt GroupQ93077
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/ID, H, O, S126Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62807 (Homo sapiens)
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PHAROS:  P62807
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UniProt GroupP62807
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere protein NK, V295Homo sapiensMutation(s): 1 
Gene Names: CENPNC16orf60ICEN32BM-309
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Find proteins for Q96H22 (Homo sapiens)
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PHAROS:  Q96H22
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UniProt GroupQ96H22
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I, T147Escherichia coli str. 'clone D i2
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J, U147Escherichia coli str. 'clone D i2
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2022-05-04
    Changes: Database references