4QLC

Crystal structure of chromatosome at 3.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.503 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 

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

  • 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 crys ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
135Drosophila melanogasterGene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Drosophila melanogasterGene Names: His4, His4r, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909 (H4, H4r)
Find proteins for P84040 (Drosophila melanogaster)
Go to UniProtKB:  P84040
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
123Drosophila melanogasterGene Names: His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865 (H2a)
Find proteins for P84051 (Drosophila melanogaster)
Go to UniProtKB:  P84051
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
122Drosophila melanogasterGene Names: His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Find proteins for P02283 (Drosophila melanogaster)
Go to UniProtKB:  P02283
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
H5
U
77Gallus gallus
Find proteins for P02259 (Gallus gallus)
Go to UniProtKB:  P02259
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (167-mer)I167Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (167-mer)J167Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, G
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.503 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 262.870α = 90.00
b = 262.870β = 90.00
c = 91.790γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
Blu-Icedata collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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