6MUP

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1016/j.cub.2019.06.062
  • Primary Citation of Related Structures:  
    6MUO, 6MUP

  • PubMed Abstract: 

    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; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein A
A, E
102Homo sapiensMutation(s): 0 
Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens)
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Go to UniProtKB:  P49450
PHAROS:  P49450
GTEx:  ENSG00000115163 
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UniProt GroupP49450
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
94Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-C
C, G
105Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ACH2AFL
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
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PHAROS:  Q93077
GTEx:  ENSG00000180573 
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UniProt GroupQ93077
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-F
D, H
92Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BF
UniProt & NIH Common Fund Data Resources
Find proteins for Q5QNW6 (Homo sapiens)
Explore Q5QNW6 
Go to UniProtKB:  Q5QNW6
GTEx:  ENSG00000203814 
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UniProt GroupQ5QNW6
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  • Reference Sequence

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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein C
K, L
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03188 (Homo sapiens)
Explore Q03188 
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PHAROS:  Q03188
GTEx:  ENSG00000145241 
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UniProt GroupQ03188
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein N
M, N
212Homo sapiensMutation(s): 0 
Gene Names: CENPNC16orf60ICEN32BM-309
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Find proteins for Q96H22 (Homo sapiens)
Explore Q96H22 
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references