PXD070910-1

PXD070910 is an original dataset announced via ProteomeXchange.

Title	Structural bases for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores
Description	HIV-1 integrase (IN) promotes encapsulation of viral genomic RNA into mature viral cores, and this function is a target for ongoing antiretroviral drug development efforts. We determined a cryo-EM structure of a primate lentiviral IN complexed with RNA, which revealed a linear filament made of IN octamer repeat units, each comprising a pair of asymmetric homotetramers. The assembly is stabilized through IN-RNA interactions primarily involving the IN C-terminal domains and RNA backbone. Remarkably, the spacing and orientation of the IN filament repeat units closely matched those of consecutive capsid (CA) hexamers within the mature CA lattice. Using cryo-EM images of native purified HIV-1 cores, we refined the structure of the IN filament as it propagates along the luminal side of the CA lattice. Each IN tetramer within the filament nestled in a CA hexamer, engaging closely with the major homology regions. Substitutions of residues involved in IN-CA contacts yielded eccentric virions with RNA nucleoids located outside of the cores. Collectively, our results establish the structural basis for the HIV 1 IN-RNA interaction and reveal that IN forms an RNA-binding module on the luminal side of the mature CA lattice.
HostingRepository	PRIDE
AnnounceDate	2025-12-04
AnnouncementXML	Submission_2025-12-04_04:24:56.019.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mark Skehel
SpeciesList	scientific name: Simian immunodeficiency virus; NCBI TaxID: NEWT:11723;
ModificationList	No PTMs are included in the dataset
Instrument	SELECT SERIES Cyclic IMS

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-18 14:34:47	ID requested
⏵ 1	2025-12-04 04:24:56	announced

Dataset with its publication pending

submitter keyword: HIV-1, HDX/MS, Integrase, Human, CryoEM

Peter Cherepanov
contact affiliation	Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
contact email	Peter.Cherepanov@crick.ac.uk
lab head
Mark Skehel
contact affiliation	Francis Crick Institute
contact email	skehelm@crick.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/12/PXD070910

PRIDE project URI

• PRIDE
  1. PXD070910
     1. Label: PRIDE project
     2. Name: Structural bases for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores