8FPI

Co-structure of the Respiratory Syncytial Virus RNA-dependent RNA polymerase with MRK-1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases.

Kleiner, V.A.Fischmann, T.O.Howe, J.A.Beshore, D.C.Eddins, M.J.Hou, Y.Mayhood, T.Klein, D.Nahas, D.D.Lucas, B.J.Xi, H.Murray, E.Ma, D.Y.Getty, K.Fearns, R.

(2023) Commun Biol 6: 649-649

  • DOI: https://doi.org/10.1038/s42003-023-04990-0
  • Primary Citation of Related Structures:  
    8FPI, 8FPJ

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults 1-3 . Therapeutic small molecule inhibitors that bind to the RSV polymerase and inhibit viral replication are being developed, but their binding sites and molecular mechanisms of action remain largely unknown 4 . Here we report a conserved allosteric inhibitory site identified on the L polymerase proteins of RSV and HMPV that can be targeted by a dual-specificity, non-nucleoside inhibitor, termed MRK-1. Cryo-EM structures of the inhibitor in complexes with truncated RSV and full-length HMPV polymerase proteins provide a structural understanding of how MRK-1 is active against both viruses. Functional analyses indicate that MRK-1 inhibits conformational changes necessary for the polymerase to engage in RNA synthesis initiation and to transition into an elongation mode. Competition studies reveal that the MRK-1 binding pocket is distinct from that of a capping inhibitor with an overlapping resistance profile, suggesting that the polymerase conformation bound by MRK-1 may be distinct from that involved in mRNA capping. These findings should facilitate optimization of dual RSV and HMPV replication inhibitors and provide insights into the molecular mechanisms underlying their polymerase activities.


  • Organizational Affiliation

    Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L1,497Human respiratory syncytial virus A2Mutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.375 (PDB Primary Data)
UniProt
Find proteins for P28887 (Human respiratory syncytial virus A (strain A2))
Explore P28887 
Go to UniProtKB:  P28887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28887
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoprotein
B, C, D, E
256Human respiratory syncytial virus A2Mutation(s): 0 
UniProt
Find proteins for P03421 (Human respiratory syncytial virus A (strain A2))
Explore P03421 
Go to UniProtKB:  P03421
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03421
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y6L (Subject of Investigation/LOI)
Query on Y6L

Download Ideal Coordinates CCD File 
F [auth A]4-(2-aminopropan-2-yl)-N'-[4-(cyclopropyloxy)-3-methoxybenzoyl]-6-(4-fluorophenyl)pyridine-2-carbohydrazide
C26 H27 F N4 O4
RLLFSRLPEMDZNU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description