Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.51 kDa 
• Atom Count: 1737 
• Modelled Residue Count: 181 
• Deposited Residue Count: 191 
• Unique protein chains: 1

4ZQQ

Apo form of influenza strain H1N1 polymerase acidic subunit N-terminal region

• PDB DOI: 10.2210/pdb4ZQQ/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-11 Released: 2015-06-03 
• Deposition Author(s): Fudo, S., Yamamoto, N., Nukaga, M., Odagiri, T., Tashiro, M., Neya, S., Hoshino, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit.

Fudo, S., Yamamoto, N., Nukaga, M., Odagiri, T., Tashiro, M., Hoshino, T.

(2016) Biochemistry 55: 2646-2660

• PubMed: 27088785 
• DOI: 10.1021/acs.biochem.5b01087
• Primary Citation of Related Structures:  
  4ZHZ, 4ZI0, 4ZQQ, 5FDD, 5FDG, 5I13


• PubMed Abstract: 
  

Influenza viruses are global threat to humans, and the development of new antiviral agents are still demanded to prepare for pandemics and to overcome the emerging resistance to the current drugs. Influenza polymerase acidic protein N-terminal domain (PAN) has endonuclease activity and is one of the appropriate targets for novel antiviral agents. First, we performed X-ray cocrystal analysis on the complex structures of PAN with two endonuclease inhibitors. The protein crystallization and the inhibitor soaking were done at pH 5.8. The binding modes of the two inhibitors were different from a common binding mode previously reported for the other influenza virus endonuclease inhibitors. We additionally clarified the complex structures of PAN with the same two endonuclease inhibitors at pH 7.0. In one of the crystal structures, an additional inhibitor molecule, which chelated to the two metal ions in the active site, was observed. On the basis of the crystal structures at pH 7.0, we carried out 100 ns molecular dynamics (MD) simulations for both of the complexes. The analysis of simulation results suggested that the binding mode of each inhibitor to PAN was stable in spite of the partial deviation of the simulation structure from the crystal one. Furthermore, crystal structure analysis and MD simulation were performed for PAN in complex with an inhibitor, which was already reported to have a high compound potency for comparison. The findings on the presence of multiple binding sites at around the PAN substrate-binding pocket will provide a hint for enhancing the binding affinity of inhibitors.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein,Polymerase acidic protein	A	191	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for P03433 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03433  Go to UniProtKB:  P03433

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.333	α = 90
b = 66.333	β = 90
c = 127.338	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-11 
• Released Date: 2015-06-03 
Deposition Author(s): Fudo, S., Yamamoto, N., Nukaga, M., Odagiri, T., Tashiro, M., Neya, S., Hoshino, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	24590548

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Database references, Derived calculations