Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 46.63 kDa 
• Atom Count: 3329 
• Residue Count: 399 
• Unique protein chains: 1

5DOC

Crystal structure of the Human Cytomegalovirus UL53 subunit of the NEC

• DOI: 10.2210/pdb5DOC/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Human herpesvirus 5 strain AD169
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-11 Released: 2015-11-25 
• Deposition Author(s): Lye, M.F., El Omari, K., Filman, D.J., Hogle, J.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Unexpected features and mechanism of heterodimer formation of a herpesvirus nuclear egress complex.

Lye, M.F., Sharma, M., El Omari, K., Filman, D.J., Schuermann, J.P., Hogle, J.M., Coen, D.M.

(2015) EMBO J 34: 2937-2952

• PubMed: 26511021 
• DOI: 10.15252/embj.201592651
• Primary Citation of Related Structures:  
  5DOC, 5DOB, 5DOE


• PubMed Abstract: 
  

Herpesvirus nucleocapsids escape from the nucleus in a process orchestrated by a highly conserved, viral nuclear egress complex. In human cytomegalovirus, the complex consists of two proteins, UL50 and UL53. We solved structures of versions of UL53 and the complex by X-ray crystallography. The UL53 structures, determined at 1.93 and 3.0 Å resolution, contained unexpected features including a Bergerat fold resembling that found in certain nucleotide-binding proteins, and a Cys3His zinc finger. Substitutions of zinc-coordinating residues decreased UL50-UL53 co-localization in transfected cells, and, when incorporated into the HCMV genome, ablated viral replication. The structure of the complex, determined at 2.47 Å resolution, revealed a mechanism of heterodimerization in which UL50 clamps onto helices of UL53 like a vise. Substitutions of particular residues on the interaction interface disrupted UL50-UL53 co-localization in transfected cells and abolished virus production. The structures and the identification of contacts can be harnessed toward the rational design of novel and highly specific antiviral drugs and will aid in the detailed understanding of nuclear egress.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion egress protein UL31 homolog	A, B	203	Human herpesvirus 5 strain AD169	Mutation(s): 0  Gene Names: UL53, NEC1
Find proteins for P16794 (Human cytomegalovirus (strain AD169)) Explore P16794  Go to UniProtKB:  P16794

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.8	α = 91
b = 50.3	β = 103
c = 63	γ = 108

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-09-11 
• Released Date: 2015-11-25 
Deposition Author(s): Lye, M.F., El Omari, K., Filman, D.J., Hogle, J.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI026077

Revision History 

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence