6MWN

Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.838 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.

Koirala, D.Shao, Y.Koldobskaya, Y.Fuller, J.R.Watkins, A.M.Shelke, S.A.Pilipenko, E.V.Das, R.Rice, P.A.Piccirilli, J.A.

(2019) Nat Commun 10: 3629-3629

  • DOI: 10.1038/s41467-019-11585-z

  • PubMed Abstract: 
  • Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES dom ...

    Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment-a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.


    Organizational Affiliation

    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab HAVx Heavy Chain
C, H
258N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab HAVx Light Chain
D, L
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
HAV dV RNA (92-MER)A,B92Hepatovirus A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A, B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.838 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.149α = 90.00
b = 100.582β = 90.00
c = 236.594γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
Aimlessdata scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01AI081987
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01GM102489

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references