6PZQ

Structure of the human respiratory syncytial virus M2-1 protein in complex with a short positive-sense gene-end RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA.

Gao, Y., Cao, D., Pawnikar, S., John, K.P., Ahn, H.M., Hill, S., Ha, J.M., Parikh, P., Ogilvie, C., Swain, A., Yang, A., Bell, A., Salazar, A., Miao, Y., Liang, B.

(2020) Structure 28: 979

  • DOI: 10.1016/j.str.2020.07.001
  • Primary Citation of Related Structures:  
    6PZQ

  • PubMed Abstract: 

    • The M2-1 protein of human respiratory syncytial virus (HRSV) is a transcription anti-terminator that regulates the processivity of the HRSV RNA-dependent RNA polymerase (RdRP). Here, we report a crystal structure of HRSV M2-1 bound to a short positive-sense gene-end RNA (SH7) at 2 ...

    The M2-1 protein of human respiratory syncytial virus (HRSV) is a transcription anti-terminator that regulates the processivity of the HRSV RNA-dependent RNA polymerase (RdRP). Here, we report a crystal structure of HRSV M2-1 bound to a short positive-sense gene-end RNA (SH7) at 2.7 Å resolution. We identified multiple critical residues of M2-1 involved in RNA interaction and examined their roles using mutagenesis and MicroScale Thermophoresis (MST) assay. We found that hydrophobic residue Phe23 is indispensable for M2-1 to recognize the base of RNA. We also captured spontaneous binding of RNA (SH7) to M2-1 in all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method. Both experiments and simulations revealed that the interactions of RNA with two separate domains of M2-1, the zinc-binding domain (ZBD) and the core domain (CD), are independent of each other. Collectively, our results provided a structural basis for RNA recognition by HRSV M2-1.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA. Electronic address: bo.liang@emory.edu.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Matrix M2-1 A, B, C, D194Human respiratory syncytial virus A2Mutation(s): 0 
Gene Names: M2-1
Find proteins for P04545 (Human respiratory syncytial virus A (strain A2))
Explore P04545 
Go to UniProtKB:  P04545
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')I, J7Human respiratory syncytial virus A2
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.225 
    • R-Value Observed: 0.228 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 94.75α = 90
    b = 94.75β = 90
    c = 199.63γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    PHASERphasing
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesR01GM130950

    Revision History  (Full details and data files)

    • Version 1.0: 2020-08-05
      Type: Initial release
    • Version 1.1: 2020-09-16
      Changes: Database references