Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome

  1. Qianglin Fang
  2. Ping Chen
  3. Mingzhu Wang
  4. Junnan Fang
  5. Na Yang
  6. Guohong Li  Is a corresponding author
  7. Rui-Ming Xu  Is a corresponding author
  1. Chinese Academy of Sciences, China
  2. University of Chinese Academy of Sciences, China
4 figures and 1 table

Figures

Figure 1 with 1 supplement
Structure of the IE1-CTD–NCP complex.

(A) Location of the IE1-CTD binding site on the acidic patch of the nucleosomal surface. The histone octamer is shown as a surface representation colored according to electrostatic potential …

https://doi.org/10.7554/eLife.11911.003
Figure 1—figure supplement 1
An omit electron density map of the bound IE1-CTD.

A stereo view of the simulated annealing (Fo-Fc) omit map showing the presence of IE1-CTD. The map is contoured at 2.5 σ level. A stick model of IE1-CTD is superimposed.

https://doi.org/10.7554/eLife.11911.004
Comparison of protein binding modes to the acidic patch of NCP.

All NCP-binding peptides or protein segments, shown in a stick model superimposed onto a cartoon representation of the backbone, were superimposed onto the structure of NCP, shown in a surface …

https://doi.org/10.7554/eLife.11911.005
Figure 3 with 1 supplement
ITC measurements of peptide-NCP binding affinities.

(A–G) Raw data and fitting curves of the integrated data for the indicated peptides and NCPs are shown together with the derived KD values and fitting errors.

https://doi.org/10.7554/eLife.11911.006
Figure 3—figure supplement 1
Binding of full-length IE1 to NCP.

Bindings of full-length IE1 (A), IE1-CTD (B), and IE1 lacking CTD (C) are measured by ITC at 150 mM NaCl concentration.

https://doi.org/10.7554/eLife.11911.007
Figure 4 with 1 supplement
Influence of IE1-CTD on higher-order chromatin structure.

(A) AUC analyses showing that IE1-CTD has little effect on the folding of the 10-nm nucleosomal array. Green and black data points represent that of 10-nm nucleosomal arrays in the absence and …

https://doi.org/10.7554/eLife.11911.008
Figure 4—figure supplement 1
Assessment of the quality of reconstituted nucleosomal array.

(A) Nucleosomal arrays corresponding to ~1 μg DNA were cleaved with indicated amount of micrococcal nuclease (MNase). (B) EM analysis of the reconstituted nucleosomal array (Bar: 100 nm).

https://doi.org/10.7554/eLife.11911.009

Tables

Table 1

Statistics of crystallographic analysis.

https://doi.org/10.7554/eLife.11911.010
Data collection statistics
wavelength (Å)1.0308
space groupP212121
unit cell (Å)a = 106.70, b = 109.47, c = 181.98
resolution (Å)30.00–2.80 (2.90–2.80)
Rmerge0.133 (0.611)
I/σI12.5 (3.3)
Completeness (%)99.9 (100.0)
Total/Unique reflections346679/52496
Refinement statistics
Rwork/Rfree0.195/0.244
rmsd bonds (Å)0.008
rmsd angles (º)0.935
No. of Atoms
 Protein6116
 DNA5982
 Peptide104
 Ion4
 Water230
B factor (Å2)
 Protein35.9
 DNA87.8
 Peptide56.9
 Ion47.5
 Water36.0
Ramachandran plot
 favored750 (98.7%)
 allowed8 (1.1%)
 outlier2 (0.3%)

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