8R6U | pdb_00008r6u

Structure of the SFTSV L protein in a transcription-priming state without capped RNA [TRANSCRIPTION-PRIMING (in vitro)]


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural snapshots of phenuivirus cap-snatching and transcription.

Williams, H.M.Thorkelsson, S.R.Vogel, D.Busch, C.Milewski, M.Cusack, S.Grunewald, K.Quemin, E.R.J.Rosenthal, M.

(2024) Nucleic Acids Res 52: 6049-6065

  • DOI: https://doi.org/10.1093/nar/gkae330
  • Primary Citation Related Structures: 
    8R6U, 8R6W, 8R6Y

  • PubMed Abstract: 

    Severe fever with thrombocytopenia syndrome virus (SFTSV) is a human pathogen that is now endemic to several East Asian countries. The viral large (L) protein catalyzes viral transcription by stealing host mRNA caps via a process known as cap-snatching. Here, we establish an in vitro cap-snatching assay and present three high-quality electron cryo-microscopy (cryo-EM) structures of the SFTSV L protein in biologically relevant, transcription-specific states. In a priming-state structure, we show capped RNA bound to the L protein cap-binding domain (CBD). The L protein conformation in this priming structure is significantly different from published replication-state structures, in particular the N- and C-terminal domains. The capped-RNA is positioned in a way that it can feed directly into the RNA-dependent RNA polymerase (RdRp) ready for elongation. We also captured the L protein in an early-elongation state following primer-incorporation demonstrating that this priming conformation is retained at least in the very early stages of primer extension. This structural data is complemented by in vitro biochemical and cell-based assays. Together, these insights further our mechanistic understanding of how SFTSV and other bunyaviruses incorporate stolen host mRNA fragments into their viral transcripts thereby allowing the virus to hijack host cell translation machinery.


  • Organizational Affiliation
    • Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 262.11 kDa 
  • Atom Count: 13,408 
  • Modeled Residue Count: 1,609 
  • Deposited Residue Count: 2,166 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,084SFTS virus AH12Mutation(s): 1 
EC: 3.1 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for I0DF35 (Dabie bandavirus)
Explore I0DF35 
Go to UniProtKB:  I0DF35
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI0DF35
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA primerB [auth P],
E
20SFTS virus AH12
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*UP*GP*GP*GP*CP*GP*GP*UP*CP*UP*UP*UP*GP*UP*GP*U)-3')C [auth T]26SFTS virus AH12
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA primer tail-endD [auth G]16SFTS virus AH12
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leibniz AssociationGermanyK72/2017
German Research Foundation (DFG)GermanyNST 152/772-1, 774-1, 775-1 and 776-1
German Federal Ministry for Education and ResearchGermany01KI2019

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Database references