PXD048268

PXD048268 is an original dataset announced via ProteomeXchange.

Title	Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment
Description	Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5 . Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
HostingRepository	PRIDE
AnnounceDate	2026-08-17
AnnouncementXML	Submission_2026-08-16_18:46:54.028.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Olexandr Dybkov
SpeciesList	scientific name: Pyrococcus furiosus; NCBI TaxID: NEWT:2261;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-05 00:58:29	ID requested
⏵ 1	2026-08-16 18:46:55	announced

Tar, ă, u D, Gr, ü, nberger F, Pilsl M, Reichelt R, Hei, ß F, K, ö, nig S, Urlaub H, Hausner W, Engel C, Grohmann D, Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment. Nucleic Acids Res, 52(10):6017-6035(2024) [pubmed]

10.1093/nar/gkae282;

submitter keyword: transcription, cryo-EM,Archaea, RNA polymerase, Spt4/5, transcription elongation

Henning Urlaub
contact affiliation	Bioanalytical Mass Spectrometry Group Max Planck Institute for Multidisciplinary Sciences Germany Bioanalytics Institute for Clinical Chemistry University Medical Center Goettingen Germany
contact email	henning.urlaub@mpinat.mpg.de
lab head
Olexandr Dybkov
contact affiliation	Max Planck Institute for Multidisciplinary Sciences
contact email	odybkov@gwdg.de
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/2026/08/PXD048268

PRIDE project URI

• PRIDE
  1. PXD048268
     1. Label: PRIDE project
     2. Name: Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment