6TEM

CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends.

Boopathi, R.Danev, R.Khoshouei, M.Kale, S.Nahata, S.Ramos, L.Angelov, D.Dimitrov, S.Hamiche, A.Petosa, C.Bednar, J.

(2020) Nucleic Acids Res 48: 5735-5748

  • DOI: 10.1093/nar/gkaa246
  • Primary Citation of Related Structures:  
    6TEM

  • PubMed Abstract: 
  • The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both D ...

    The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both DNA ends to be highly flexible, a feature important for CENP-A mitotic functions. However, recent cryo-EM studies of CENP-A NCP complexes comprising primarily Widom 601 DNA reported well-ordered DNA ends. Here, we report the cryo-EM structure of the CENP-A 601 NCP determined by Volta phase-plate imaging. The data reveal that one ('left') 601 DNA end is well ordered whereas the other ('right') end is flexible and partly detached from the histone core, suggesting sequence-dependent dynamics of the DNA termini. Indeed, a molecular dynamics simulation of the CENP-A 601 NCP confirmed the distinct dynamics of the two DNA extremities. Reprocessing the image data using two-fold symmetry yielded a cryo-EM map in which both DNA ends appeared well ordered, indicating that such an artefact may inadvertently arise if NCP asymmetry is lost during image processing. These findings enhance our understanding of the dynamic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be fine-tuned in a sequence-dependent manner.


    Organizational Affiliation

    Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Teaching Hospital, 128 00 Prague, Czech Republic.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AAE140Homo sapiensMutation(s): 0 
Gene Names: CENPA
Find proteins for P49450 (Homo sapiens)
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Go to UniProtKB:  P49450
NIH Common Fund Data Resources
PHAROS  P49450
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
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Go to UniProtKB:  P06897
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH125Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Widom 601 DNA (145-MER, sense)I145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Widom 601 DNA (145-MER, antisense)J145synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceChromcomp
French National Research AgencyFranceChrome
French National Research AgencyFranceChrom3D
French National Research AgencyFranceEPIVAR.Z

Revision History 

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Database references
  • Version 1.3: 2020-04-29
    Changes: Database references
  • Version 1.4: 2020-06-10
    Changes: Database references