Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome
- Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
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 …
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.
Figure 2
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 …
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.
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.
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 …
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).
Tables
Table 1
Statistics of crystallographic analysis.
| Data collection statistics | |
| wavelength (Å) | 1.0308 |
| space group | P212121 |
| unit cell (Å) | a = 106.70, b = 109.47, c = 181.98 |
| resolution (Å) | 30.00–2.80 (2.90–2.80) |
| Rmerge | 0.133 (0.611) |
| I/σI | 12.5 (3.3) |
| Completeness (%) | 99.9 (100.0) |
| Total/Unique reflections | 346679/52496 |
| Refinement statistics | |
| Rwork/Rfree | 0.195/0.244 |
| rmsd bonds (Å) | 0.008 |
| rmsd angles (º) | 0.935 |
| No. of Atoms | |
| Protein | 6116 |
| DNA | 5982 |
| Peptide | 104 |
| Ion | 4 |
| Water | 230 |
| B factor (Å2) | |
| Protein | 35.9 |
| DNA | 87.8 |
| Peptide | 56.9 |
| Ion | 47.5 |
| Water | 36.0 |
| Ramachandran plot | |
| favored | 750 (98.7%) |
| allowed | 8 (1.1%) |
| outlier | 2 (0.3%) |
