Structure of Influenza B Lee PB2 cap-binding domain bound to m7GTP

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit.

Xie, L.Wartchow, C.Shia, S.Uehara, K.Steffek, M.Warne, R.Sutton, J.Muiru, G.T.Leonard, V.H.Bussiere, D.E.Ma, X.

(2016) J Biol Chem 291: 363-370

  • DOI: https://doi.org/10.1074/jbc.M115.693051
  • Primary Citation of Related Structures:  
    5EF9, 5EFA, 5EFC

  • PubMed Abstract: 

    Influenza virus polymerase catalyzes the transcription of viral mRNAs by a process known as "cap-snatching," where the 5'-cap of cellular pre-mRNA is recognized by the PB2 subunit and cleaved 10-13 nucleotides downstream of the cap by the endonuclease PA subunit. Although this mechanism is common to both influenza A (FluA) and influenza B (FluB) viruses, FluB PB2 recognizes a wider range of cap structures including m(7)GpppGm-, m(7)GpppG-, and GpppG-RNA, whereas FluA PB2 utilizes methylated G-capped RNA specifically. Biophysical studies with isolated PB2 cap-binding domain (PB2(cap)) confirm that FluB PB2 has expanded mRNA cap recognition capability, although the affinities toward m(7)GTP are significantly reduced when compared with FluA PB2. The x-ray co-structures of the FluB PB2(cap) with bound cap analogs m(7)GTP and GTP reveal an inverted GTP binding mode that is distinct from the cognate m(7)GTP binding mode shared between FluA and FluB PB2. These results delineate the commonalities and differences in the cap-binding site between FluA and FluB PB2 and will aid structure-guided drug design efforts to identify dual inhibitors of both FluA and FluB PB2.

  • Organizational Affiliation

    From the Divisions of Protein Sciences.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2174Influenza B virus (B/Lee/1940)Mutation(s): 0 
Gene Names: PB2
Find proteins for Q9QLL6 (Influenza B virus (strain B/Lee/1940))
Explore Q9QLL6 
Go to UniProtKB:  Q9QLL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QLL6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MGT

Download Ideal Coordinates CCD File 
C11 H20 N5 O14 P3
Binding Affinity Annotations 
IDSourceBinding Affinity
MGT Binding MOAD:  5EFA Kd: 1.47e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.343α = 90
b = 46.709β = 90
c = 87.794γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations