4QLC

Crystal structure of chromatosome at 3.5 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural Mechanisms of Nucleosome Recognition by Linker Histones.

Zhou, B.R., Jiang, J., Feng, H., Ghirlando, R., Xiao, T.S., Bai, Y.

(2015) Mol Cell 33 Suppl 1: 2-3

  • DOI: 10.1016/j.molcel.2015.06.025
  • Primary Citation of Related Structures:  
    4QLC

  • PubMed Abstract: 

    • Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, the structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal ...

    Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, the structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses and previous cross-linking and fluorescence recovery after photobleach experiments, and it helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures.

    Organizational Affiliation: 

    Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: yawen@helix.nih.gov.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3 A, E135Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02299 (Drosophila melanogaster)
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Go to UniProtKB:  P02299
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 B, F102Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84040 (Drosophila melanogaster)
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Go to UniProtKB:  P84040
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A C, G123Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84051 (Drosophila melanogaster)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B D, H122Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02283 (Drosophila melanogaster)
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Go to UniProtKB:  P02283
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
H5 U77Gallus gallusMutation(s): 0 
Gene Names: H5_CHICK
Find proteins for P02259 (Gallus gallus)
Explore P02259 
Go to UniProtKB:  P02259
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (167-mer)I167Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (167-mer)J167Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download Ideal Coordinates CCD File 
A, G
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 262.87α = 90
b = 262.87β = 90
c = 91.79γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references, Derived calculations
  • Version 1.2: 2015-08-12
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Advisory, Refinement description