4WRT

Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)

• PDB DOI:  https://doi.org/10.2210/pdb4WRT/pdb
• NAKB: 4WRT

• Classification: TRANSFERASE/RNA
• Organism(s): Influenza B virus, Influenza B virus (B/Memphis/13/2003)
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2014-10-25 Released: 2014-11-19 
• Deposition Author(s): Reich, S., Guilligay, D., Pflug, A., Cusack, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Structural insight into cap-snatching and RNA synthesis by influenza polymerase.

Reich, S., Guilligay, D., Pflug, A., Malet, H., Berger, I., Crepin, T., Hart, D., Lunardi, T., Nanao, M., Ruigrok, R.W., Cusack, S.

(2014) Nature 516: 361-366

• PubMed: 25409151 
• DOI: https://doi.org/10.1038/nature14009
• Primary Citation of Related Structures:  
  4WRT, 4WSA, 4WSB


• PubMed Abstract: 
  

Influenza virus polymerase uses a capped primer, derived by 'cap-snatching' from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in situ rotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states.

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Related Citations: 

• Crystal structure of influenza A polymerase bound to the viral RNA promoter
  Pflug, A., Guilligay, D., Reich, S., Cusack, S.
  () To be published --: --

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Organizational Affiliation: 

1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 273.02 kDa 
• Atom Count: 14,972 
• Modelled Residue Count: 1,730 
• Deposited Residue Count: 2,353 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PA	C [auth A]	751	Influenza B virus (B/Memphis/13/2003)	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for Q5V8Z9 (Influenza B virus) Explore Q5V8Z9  Go to UniProtKB:  Q5V8Z9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase catalytic subunit	D [auth B]	772	Influenza B virus (B/Memphis/13/2003)	Mutation(s): 0  Gene Names: PB1 EC: 2.7.7.48
UniProt
Find proteins for Q5V8Y6 (Influenza B virus) Explore Q5V8Y6  Go to UniProtKB:  Q5V8Y6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PB2	E [auth C]	798	Influenza B virus (B/Memphis/13/2003)	Mutation(s): 0  Gene Names: PB2
UniProt
Find proteins for Q5V8X3 (Influenza B virus) Explore Q5V8X3  Go to UniProtKB:  Q5V8X3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Influenza virus polymerase vRNA promoter 3' end	A [auth R]	18	Influenza B virus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Influenza virus polymerase vRNA promoter 5' end	B [auth V]	14	Influenza B virus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.37	α = 90
b = 207.37	β = 90
c = 345.69	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Reich, S., Guilligay, D., Pflug, A., Cusack, S.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Database references
• Version 1.2: 2014-12-24
  Changes: Database references
• Version 1.3: 2019-04-03
  Changes: Data collection, Source and taxonomy