Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 57.07 kDa 
• Atom Count: 3674 
• Modelled Residue Count: 451 
• Deposited Residue Count: 501 
• Unique protein chains: 2

3CM8

A RNA polymerase subunit structure from virus

• PDB DOI: 10.2210/pdb3CM8/pdb

• Classification: RNA BINDING PROTEIN/Transferase
• Organism(s): Influenza A virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-21 Released: 2008-07-15 
• Deposition Author(s): He, X., Zhou, J., Zeng, Z., Ma, J., Zhang, R., Rao, Z., Liu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus

He, X., Zhou, J., Bartlam, M., Zhang, R., Ma, J., Lou, Z., Li, X., Li, J., Joachimiak, A., Zeng, Z., Ge, R., Rao, Z., Liu, Y.

(2008) Nature 454: 1123-1126

• PubMed: 18615018 
• DOI: 10.1038/nature07120
• Primary Citation of Related Structures:  
  3CM8


• PubMed Abstract: 
  

The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding; PA is implicated in RNA replication and proteolytic activity, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA(C), residues 257-716) in complex with the PA-binding region of PB1 (PB1(N), residues 1-25). PA(C) has a fold resembling a dragon's head with PB1(N) clamped into its open 'jaws'. PB1(N) is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1(N) to PA(C) at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA(C) with the lambda3 reovirus polymerase structure, and docking the PA(C) structure into an available low resolution electron microscopy map.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	471	Influenza A virus	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for Q9EA60 (Influenza A virus) Explore Q9EA60  Go to UniProtKB:  Q9EA60

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from RNA-directed RNA polymerase catalytic subunit	B	30	Influenza A virus	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q9WLS3 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd)) Explore Q9WLS3  Go to UniProtKB:  Q9WLS3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.942	α = 90
b = 121.942	β = 90
c = 134.594	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-21 
• Released Date: 2008-07-15 
Deposition Author(s): He, X., Zhou, J., Zeng, Z., Ma, J., Zhang, R., Rao, Z., Liu, Y.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance