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Yorodumi- PDB-7ojl: Lassa virus L protein in a pre-initiation conformation [PREINITIATION] -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ojl | |||||||||
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Title | Lassa virus L protein in a pre-initiation conformation [PREINITIATION] | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Lassa virus RNA-dependent RNA polymerase viral RNA | |||||||||
Function / homology | Function and homology information negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Lassa mammarenavirus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Kouba, T. / Vogel, D. / Thorkelsson, S. / Quemin, E. / Williams, H.M. / Milewski, M. / Busch, C. / Gunther, S. / Grunewald, K. / Rosenthal, M. / Cusack, S. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity. Authors: Tomas 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 / Abstract: 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 ...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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ojl.cif.gz | 312.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojl.ent.gz | 235.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ojl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ojl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ojl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ojl_validation.xml.gz | 54 KB | Display | |
Data in CIF | 7ojl_validation.cif.gz | 81 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojl ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojl | HTTPS FTP |
-Related structure data
Related structure data | 12955MC 7ochC 7oe3C 7oe7C 7oeaC 7oebC 7ojjC 7ojkC 7ojnC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 253656.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa mammarenavirus / Production host: Trichoplusia ni (cabbage looper) References: UniProt: A0A3S8NV63, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 6069.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lassa mammarenavirus |
#3: RNA chain | Mass: 6452.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lassa mammarenavirus |
#4: Chemical | ChemComp-MN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.253346 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119900 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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