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Structure paper

TitleConformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 7018, Year 2021
Publish dateDec 2, 2021
AuthorsTomas Kouba / Dominik Vogel / Sigurdur R Thorkelsson / Emmanuelle R J Quemin / Harry M Williams / Morlin Milewski / Carola Busch / Stephan Günther / Kay Grünewald / Maria Rosenthal / Stephen Cusack /
PubMed AbstractLassa virus is endemic in West Africa and can cause severe hemorrhagic fever. The viral L protein transcribes and replicates the RNA genome via its RNA-dependent RNA polymerase activity. Here, we ...Lassa virus is endemic in West Africa and can cause severe hemorrhagic fever. The viral L protein transcribes and replicates the RNA genome via its RNA-dependent RNA polymerase activity. Here, we present nine cryo-EM structures of the L protein in the apo-, promoter-bound pre-initiation and active RNA synthesis states. We characterize distinct binding pockets for the conserved 3' and 5' promoter RNAs and show how full-promoter binding induces a distinct pre-initiation conformation. In the apo- and early elongation states, the endonuclease is inhibited by two distinct L protein peptides, whereas in the pre-initiation state it is uninhibited. In the early elongation state, a template-product duplex is bound in the active site cavity together with an incoming non-hydrolysable nucleotide and the full C-terminal region of the L protein, including the putative cap-binding domain, is well-ordered. These data advance our mechanistic understanding of how this flexible and multifunctional molecular machine is activated.
External linksNat Commun / PubMed:34857749 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.89 Å
Structure data

EMDB-12807, PDB-7och:
Apo-structure of Lassa virus L protein (well-resolved polymerase core) [APO-CORE]
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-12860, PDB-7oe3:
Apo-structure of Lassa virus L protein (well-resolved endonuclease) [APO-ENDO]
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-12861, PDB-7oe7:
Apo-structure of Lassa virus L protein (well-resolved alpha ribbon) [APO-RIBBON]
Method: EM (single particle) / Resolution: 3.73 Å

EMDB-12862, PDB-7oea:
Lassa virus L protein bound to 3' promoter RNA (well-resolved polymerase core) [3END-CORE]
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-12863, PDB-7oeb:
Lassa virus L protein bound to 3' promoter RNA (well-resolved endonuclease) [3END-ENDO]
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-12953, PDB-7ojj:
Lassa virus L protein with endonuclease and C-terminal domains in close proximity [MID-LINK]
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-12954, PDB-7ojk:
Lassa virus L protein bound to the distal promoter duplex [DISTAL-PROMOTER]
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-12955, PDB-7ojl:
Lassa virus L protein in a pre-initiation conformation [PREINITIATION]
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-12956, PDB-7ojn:
Lassa virus L protein in an elongation conformation [ELONGATION]
Method: EM (single particle) / Resolution: 2.92 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MN:
Unknown entry

ChemComp-2KH:
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine

Source
  • lassa mammarenavirus
KeywordsVIRAL PROTEIN / Lassa virus RNA-dependent RNA polymerase viral RNA

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