8DP3

Crystal structure of coxsackievirus B3 cloverleaf RNA replication element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Literature

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.

Das, N.K.Hollmann, N.M.Vogt, J.Sevdalis, S.E.Banna, H.A.Ojha, M.Koirala, D.

(2023) Nat Commun 14: 1955-1955

  • DOI: https://doi.org/10.1038/s41467-023-37658-8
  • Primary Citation of Related Structures:  
    8DP3

  • PubMed Abstract: 

    The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6 Heavy ChainA [auth H]256synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6 Light ChainB [auth L]238synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (90-MER)C [auth R]90Coxsackievirus B3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
D [auth L]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.173α = 90
b = 48.698β = 112.92
c = 144.653γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesStart-up

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description