5E5A

Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Fang, Q.Chen, P.Wang, M.Fang, J.Yang, N.Li, G.Xu, R.M.

(2016) Elife 5

  • DOI: 10.7554/eLife.11911
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human cytomegalovirus (hCMV) immediate early 1 (IE1) protein associates with condensed chromatin of the host cell during mitosis. We have determined the structure of the chromatin-tethering domain (CTD) of IE1 bound to the nucleosome core particle, a ...

    Human cytomegalovirus (hCMV) immediate early 1 (IE1) protein associates with condensed chromatin of the host cell during mitosis. We have determined the structure of the chromatin-tethering domain (CTD) of IE1 bound to the nucleosome core particle, and discovered that IE1-CTD specifically interacts with the H2A-H2B acidic patch and impairs the compaction of higher-order chromatin structure. Our results suggest that IE1 loosens up the folding of host chromatin during hCMV infections.


    Organizational Affiliation

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
C-terminal domain of Regulatory protein IE1
K
16Human herpesvirus 5 strain TowneMutation(s): 0 
Gene Names: UL123
Find proteins for P03169 (Human cytomegalovirus (strain Towne))
Go to UniProtKB:  P03169

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (146-MER)I, J146Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
C, D, E, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.7α = 90
b = 109.474β = 90
c = 181.976γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry Ministry of Science and Technologyof Science and TechnologyChina2015CB856200
National Natural Science Foundation of ChinaChina31430018
National Natural Science Foundation of ChinaChina31521002
National Natural Science Foundation of ChinaChina91219202
National Natural Science Foundation of ChinaChina31471218
National Natural Science Foundation of ChinaChina31210103914
Strategic Priority Research Program of Chinese Academy of SciencesChinaXDB08010100

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence