5E5A

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

• PDB DOI: https://doi.org/10.2210/pdb5E5A/pdb
• NAKB: 5E5A

• Classification: PROTEIN BINDING/VIRAL PROTEIN/DNA
• Organism(s): Homo sapiens, Xenopus laevis, Human herpesvirus 5 strain Towne
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-08 Released: 2016-02-03 
• Deposition Author(s): Fang, Q., Chen, P., Wang, M., Fang, J., Yang, N., Li, G., Xu, R.M.
• Funding Organization(s): Ministry Ministry of Science and Technologyof Science and Technology, National Natural Science Foundation of China, Strategic Priority Research Program of Chinese Academy of Sciences

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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 

Starting Model: experimental

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

• PubMed: 26812545 
• DOI: https://doi.org/10.7554/eLife.11911
• Primary Citation of Related Structures:  
  5E5A


• 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, 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.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A7B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 201.1 kDa 
• Atom Count: 12,407 
• Modelled Residue Count: 1,070 
• Deposited Residue Count: 1,292 
• Unique protein chains: 5
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	C [auth A], G [auth E]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth C], I [auth G]	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591
UniProt
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	F [auth D], J [auth H]	123	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal domain of Regulatory protein IE1	K	16	Human herpesvirus 5 strain Towne	Mutation(s): 0
UniProt
Find proteins for P03169 (Human cytomegalovirus (strain Towne)) Explore P03169  Go to UniProtKB:  P03169

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	A [auth I], B [auth J]	146	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	L [auth I], M [auth C], N [auth D], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 106.7	α = 90
b = 109.474	β = 90
c = 181.976	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Fang, Q., Chen, P., Wang, M., Fang, J., Yang, N., Li, G., Xu, R.M.

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Funding Organization	Location	Grant Number
Ministry Ministry of Science and Technologyof Science and Technology	China	2015CB856200
National Natural Science Foundation of China	China	31430018
National Natural Science Foundation of China	China	31521002
National Natural Science Foundation of China	China	91219202
National Natural Science Foundation of China	China	31471218
National Natural Science Foundation of China	China	31210103914
Strategic Priority Research Program of Chinese Academy of Sciences	China	XDB08010100

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
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description