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Yorodumi- EMDB-12956: Lassa virus L protein in an elongation conformation [ELONGATION] -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12956 | |||||||||
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Title | Lassa virus L protein in an elongation conformation [ELONGATION] | |||||||||
Map data | Lassa virus L protein in an elongation conformation [ELONGATION] | |||||||||
Sample |
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Keywords | Lassa virus RNA-dependent RNA polymerase viral RNA / VIRAL PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
Authors | Kouba T / Vogel D | |||||||||
Funding support | Germany, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12956.map.gz | 61.5 MB | EMDB map data format | |
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Header (meta data) | emd-12956-v30.xml emd-12956.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12956_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_12956.png | 100.5 KB | ||
Filedesc metadata | emd-12956.cif.gz | 7.6 KB | ||
Others | emd_12956_additional_1.map.gz emd_12956_half_map_1.map.gz emd_12956_half_map_2.map.gz | 117.3 MB 98.4 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12956 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12956 | HTTPS FTP |
-Validation report
Summary document | emd_12956_validation.pdf.gz | 889.7 KB | Display | EMDB validaton report |
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Full document | emd_12956_full_validation.pdf.gz | 889.3 KB | Display | |
Data in XML | emd_12956_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_12956_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12956 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12956 | HTTPS FTP |
-Related structure data
Related structure data | 7ojnMC 7ochC 7oe3C 7oe7C 7oeaC 7oebC 7ojjC 7ojkC 7ojlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12956.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Lassa virus L protein in an elongation conformation [ELONGATION] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_12956_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12956_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12956_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA-directed RNA polymerase L Lassa mammarenavirus
+Supramolecule #1: RNA-directed RNA polymerase L Lassa mammarenavirus
+Supramolecule #2: RNA-directed RNA polymerase L
+Supramolecule #3: 5' RNA, 3' RNA
+Supramolecule #4: product RNA
+Macromolecule #1: RNA-directed RNA polymerase L
+Macromolecule #2: 5' RNA
+Macromolecule #3: 3' RNA
+Macromolecule #4: product RNA
+Macromolecule #5: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phos...
+Macromolecule #6: MANGANESE (II) ION
+Macromolecule #7: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |