7K61

Cryo-EM structure of 197bp nucleosome aided by scFv


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.

Zhou, B.R.Feng, H.Kale, S.Fox, T.Khant, H.de Val, N.Ghirlando, R.Panchenko, A.R.Bai, Y.

(2021) Mol Cell 81: 166-182.e6

  • DOI: https://doi.org/10.1016/j.molcel.2020.10.038
  • Primary Citation of Related Structures:  
    7K5X, 7K5Y, 7K60, 7K61, 7K63

  • PubMed Abstract: 

    The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.


  • Organizational Affiliation

    Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
136Homo sapiensMutation(s): 0 
Gene Names: 
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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
scFv20K [auth M],
L [auth N]
270Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (197-MER)197Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (197-MER)197Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references