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Yorodumi- EMDB-22270: Structure of SARS-CoV-2 replication/transcription complex bound t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22270 | |||||||||
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Title | Structure of SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(1)-RTC | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Chen J / Malone B / Llewellyn EC / Campbell EA / Darst SA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2020 Title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex. Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Ed Eng / Hasan Vatandaslar / Brian T Chait / Tarun Kapoor / ...Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Ed Eng / Hasan Vatandaslar / Brian T Chait / Tarun Kapoor / Seth A Darst / Elizabeth A Campbell / Abstract: SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a ...SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development. | |||||||||
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_22270.map.gz | 118.2 MB | EMDB map data format | |
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Header (meta data) | emd-22270-v30.xml emd-22270.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22270_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_22270.png | 37.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22270 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22270 | HTTPS FTP |
-Validation report
Summary document | emd_22270_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
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Full document | emd_22270_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_22270_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22270 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22270 | HTTPS FTP |
-Related structure data
Related structure data | 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_22270.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 replication/transcription complex bound to nsp13 helic...
Entire | Name: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(1)-RTC |
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Components |
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-Supramolecule #1: SARS-CoV-2 replication/transcription complex bound to nsp13 helic...
Supramolecule | Name: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(1)-RTC type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
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: 65.0 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 |