PXD071261

PXD071261 is an original dataset announced via ProteomeXchange.

Title	A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase
Description	Alphaviruses are mosquito-vectored, positive-strand RNA viruses causing rheumatic and neurological diseases. Like all RNA viruses, they encode an RNA-dependent RNA polymerase (RdRp, nsP4). Purification of an nsP4 derivative capable of processive RNA synthesis from a heteropolymeric template has been unsuccessful. Prior studies indicated O’nyong-nyong virus (ONNV) nsP4 is soluble and requires additional non-structural proteins for activity. We performed biochemical and biophysical characterization of ONNV nsP4, including analytical ultracentrifugation and small-angle X-ray scattering (SAXS), revealing an extended conformation inconsistent with AlphaFold predictions of a compact structure. Fold switching was required for the extended conformation. Hydrogen-deuterium exchange mass spectrometry confirmed the fold-switched, extended state. Phylogenetic analysis showed conservation of residues contributing to both extended and compact states, implying functional roles for each. The extended form exhibited weak RNA binding and no polymerase activity on primed templates. The SAXS envelope of a precursor containing 50 amino acids from the nsP3 C-terminus (CT50-P34) matched the compact state. We propose precursor forms adopt the compact conformation. At the replication site, proteolytic cleavage would convert the precursor to an active polymerase. Polymerase dissociation upon completion of synthesis would induce fold switching to the inactive, extended state, precluding cytoplasmic activity that would activate intracellular immune responses.
HostingRepository	PRIDE
AnnounceDate	2026-01-06
AnnouncementXML	Submission_2026-01-06_06:46:25.309.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sean Braet
SpeciesList	scientific name: Alphavirus; NCBI TaxID: NEWT:11019;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-26 08:09:03	ID requested
⏵ 1	2026-01-06 06:46:25	announced

Dataset with its publication pending

submitter keyword: fold switching,HDXMS, alphavirus, RNA-dependent RNA polymerase, RNA virus

Ganesh S. Anand
contact affiliation	The Pennsylvania State University, Department of Chemistry
contact email	gsa5089@psu.edu
lab head
Sean Braet
contact affiliation	Penn State
contact email	smb6745@psu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD071261
     1. Label: PRIDE project
     2. Name: A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase