7V90

Telomeric mononucleosome


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 1.3 of the entry. See complete history


Literature

Columnar structure of human telomeric chromatin.

Soman, A.Wong, S.Y.Korolev, N.Surya, W.Lattmann, S.Vogirala, V.K.Chen, Q.Berezhnoy, N.V.van Noort, J.Rhodes, D.Nordenskiold, L.

(2022) Nature 609: 1048-1055

  • DOI: https://doi.org/10.1038/s41586-022-05236-5
  • Primary Citation of Related Structures:  
    7V90, 7V96, 7V9C, 7V9J, 7V9K, 7V9S, 7VA4

  • PubMed Abstract: 

    Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response 1-5 . Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat  length that comprised about 132 bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
136Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
130Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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UniProt GroupP04908
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-K
D, H
99Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
Explore O60814 
Go to UniProtKB:  O60814
PHAROS:  O60814
GTEx:  ENSG00000197903 
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UniProt GroupO60814
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-mer)145Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-mer)145Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-07-27 
  • Deposition Author(s): Soman, A.

Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Database references
  • Version 1.3: 2022-10-12
    Changes: Database references