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)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.81 kDa 
• Atom Count: 7056 
• Residue Count: 870 
• Unique protein chains: 1

3N4Q

Human cytomegalovirus terminase nuclease domain, Mn soaked

• DOI: 10.2210/pdb3N4Q/pdb

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


• Deposited: 2010-05-22 Released: 2010-10-13 
• Deposition Author(s): Nadal, M., Mas, P.J., Blanco, A.G., Arnan, C., Sola, M., Hart, D.J., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.283 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Literature

Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.

Nadal, M., Mas, P.J., Blanco, A.G., Arnan, C., Sola, M., Hart, D.J., Coll, M.

(2010) Proc Natl Acad Sci U S A 107: 16078-16083

• PubMed: 20805464 
• DOI: 10.1073/pnas.1007144107
• Primary Citation of Related Structures:  
  3N4Q, 3N4P


• PubMed Abstract: 
  

During viral replication, herpesviruses package their DNA into the procapsid by means of the terminase protein complex. In human cytomegalovirus (herpesvirus 5), the terminase is composed of subunits UL89 and UL56. UL89 cleaves the long DNA concatemers into unit-length genomes of appropriate length for encapsidation. We used ESPRIT, a high-throughput screening method, to identify a soluble purifiable fragment of UL89 from a library of 18,432 randomly truncated ul89 DNA constructs. The purified protein was crystallized and its three-dimensional structure was solved. This protein corresponds to the key nuclease domain of the terminase and shows an RNase H/integrase-like fold. We demonstrate that UL89-C has the capacity to process the DNA and that this function is dependent on Mn(2+) ions, two of which are located at the active site pocket. We also show that the nuclease function can be inactivated by raltegravir, a recently approved anti-AIDS drug that targets the HIV integrase.

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Organizational Affiliation: 

Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TERMINASE SUBUNIT UL89 PROTEIN	A, B, C, D	279	Human herpesvirus 5 strain Towne	Mutation(s): 0  EC: 3.1
Find proteins for P16732 (Human cytomegalovirus (strain AD169)) Explore P16732  Go to UniProtKB:  P16732

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, B, C, D	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.283 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.7	α = 90
b = 88.1	β = 90
c = 190.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-22 
• Released Date: 2010-10-13 
Deposition Author(s): Nadal, M., Mas, P.J., Blanco, A.G., Arnan, C., Sola, M., Hart, D.J., Coll, M.

Revision History 

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance