6MUO

CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Structure of the Human Core Centromeric Nucleosome Complex.

Allu, P.K.Dawicki-McKenna, J.M.Van Eeuwen, T.Slavin, M.Braitbard, M.Xu, C.Kalisman, N.Murakami, K.Black, B.E.

(2019) Curr.Biol. 29: 2625-2639.e5

  • DOI: 10.1016/j.cub.2019.06.062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Centromeric nucleosomes are at the interface of the┬áchromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP ...

    Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP-C (through its central domain; CD) and CENP-N (through its N-terminal domain; NT). CENP-C can engage nucleosomes through two domains: the CD and the CENP-C motif (CM). CENP-C CD is part of the CCNC by virtue of its high specificity for CENP-A nucleosomes and ability to stabilize CENP-A at the centromere. CENP-C CM is thought to engage a neighboring nucleosome, either one containing conventional H3 or CENP-A, and a crystal structure of a nucleosome complex containing two copies of CENP-C CM was reported. Recent structures containing a single copy of CENP-N NT bound to the CENP-A nucleosome in the absence of CENP-C were reported. Here, we find that one copy of CENP-N is lost for every two copies of CENP-C on centromeric chromatin just prior to kinetochore formation. We present the structures of symmetric and asymmetric forms of the CCNC that vary in CENP-N stoichiometry. Our structures explain how the central domain of CENP-C achieves its high specificity for CENP-A nucleosomes and how CENP-C and CENP-N sandwich the histone H4 tail. The natural centromeric DNA path in our structures corresponds to symmetric surfaces for CCNC assembly, deviating from what is observed in prior structures using artificial sequences. At mitosis, we propose that CCNC asymmetry accommodates its asymmetric connections at the chromosome/kinetochore interface. VIDEO ABSTRACT.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: blackbe@pennmedicine.upenn.edu.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein A
A, E
102Homo sapiensMutation(s): 0 
Gene 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
94Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-C
C, G
105Homo sapiensMutation(s): 0 
Gene 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 type 2-F
D, H
92Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BF
Find proteins for Q5QNW6 (Homo sapiens)
Go to Gene View: HIST2H2BF
Go to UniProtKB:  Q5QNW6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Centromere protein C
K, L
20Homo sapiensMutation(s): 0 
Gene Names: CENPC (CENPC1, ICEN7)
Find proteins for Q03188 (Homo sapiens)
Go to Gene View: CENPC
Go to UniProtKB:  Q03188
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Centromere protein N
M
212Homo sapiensMutation(s): 0 
Gene Names: CENPN (C16orf60, ICEN32)
Find proteins for Q96H22 (Homo sapiens)
Go to Gene View: CENPN
Go to UniProtKB:  Q96H22
Entity ID: 5
MoleculeChainsLengthOrganism
DNA/RNA (147-MER)I147Homo sapiens
Entity ID: 6
MoleculeChainsLengthOrganism
DNA/RNA (147-MER)J147Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM123233 GM130302

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-08-14
    Type: Data collection, Database references
  • Version 1.3: 2019-09-04
    Type: Data collection, Database references
  • Version 2.0: 2019-10-02
    Type: Data collection, Polymer sequence
  • Version 2.1: 2019-12-18
    Type: Author supporting evidence