|Entry||Database: PDB / ID: 6nus|
|Title||SARS-Coronavirus NSP12 bound to NSP8 co-factor|
|Keywords||VIRAL PROTEIN / coronavirus / polymerase / non-structural protein|
|Function / homology|
Function and homology information
modulation by virus of host autophagy / positive regulation of ubiquitin-specific protease activity / suppression by virus of host translation / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / Lys48-specific deubiquitinase activity / cytoplasmic viral factory / omega peptidase activity / 3'-5'-exoribonuclease activity / suppression by virus of host IRF3 activity ...modulation by virus of host autophagy / positive regulation of ubiquitin-specific protease activity / suppression by virus of host translation / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / Lys48-specific deubiquitinase activity / cytoplasmic viral factory / omega peptidase activity / 3'-5'-exoribonuclease activity / suppression by virus of host IRF3 activity / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / transcription, RNA-templated / suppression by virus of host ISG15 activity / 7-methylguanosine mRNA capping / viral genome replication / host cell endoplasmic reticulum-Golgi intermediate compartment / positive stranded viral RNA replication / suppression by virus of host NF-kappaB transcription factor activity / modulation by virus of host protein ubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral transcription / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / helicase activity / single-stranded RNA binding / thiol-dependent ubiquitinyl hydrolase activity / ubiquitinyl hydrolase 1 / Transferases; Transferring one-carbon groups; Methyltransferases / DNA helicase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / methyltransferase activity / viral protein processing / host cell perinuclear region of cytoplasm / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / double-stranded RNA binding / RNA helicase / methylation / induction by virus of host autophagy / RNA-directed RNA polymerase / endonuclease activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA helicase activity / RNA-directed 5'-3' RNA polymerase activity / Hydrolases; Acting on ester bonds / transcription, DNA-templated / RNA binding / zinc ion binding / integral component of membrane / ATP binding / identical protein binding
nsp8 replicase / Non-structural protein NSP9, coronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP1, betacoronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / in:ipr014827: / Peptidase C16, coronavirus / (+) RNA virus helicase core domain ...nsp8 replicase / Non-structural protein NSP9, coronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP1, betacoronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / in:ipr014827: / Peptidase C16, coronavirus / (+) RNA virus helicase core domain / RNA polymerase, N-terminal, coronaviral / Non-structural protein NSP11, coronavirus / Non-structural protein NSP16, coronavirus-like / Peptidase S1, PA clan / Peptidase C30, coronavirus / RNA-directed RNA polymerase, catalytic domain / Macro domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Coronaviridae zinc-binding domain / Non-structural protein NSP1 superfamily, betacoronavirus / Coronavirus RPol N-terminus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / P-loop containing nucleoside triphosphate hydrolase / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase
Replicase polyprotein 1a / Replicase polyprotein 1ab
|Biological species||Human SARS coronavirus|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å|
|Authors||Kirchdoerfer, R.N. / Ward, A.B.|
|Funding support|| United States, 2items |
|Citation||Journal: Nat Commun / Year: 2019|
Title: Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors.
Authors: Robert N Kirchdoerfer / Andrew B Ward /
Abstract: Recent history is punctuated by the emergence of highly pathogenic coronaviruses such as SARS- and MERS-CoV into human circulation. Upon infecting host cells, coronaviruses assemble a multi-subunit ...Recent history is punctuated by the emergence of highly pathogenic coronaviruses such as SARS- and MERS-CoV into human circulation. Upon infecting host cells, coronaviruses assemble a multi-subunit RNA-synthesis complex of viral non-structural proteins (nsp) responsible for the replication and transcription of the viral genome. Here, we present the 3.1 Å resolution structure of the SARS-CoV nsp12 polymerase bound to its essential co-factors, nsp7 and nsp8, using single particle cryo-electron microscopy. nsp12 possesses an architecture common to all viral polymerases as well as a large N-terminal extension containing a kinase-like fold and is bound by two nsp8 co-factors. This structure illuminates the assembly of the coronavirus core RNA-synthesis machinery, provides key insights into nsp12 polymerase catalysis and fidelity and acts as a template for the design of novel antiviral therapeutics.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein|| |
Mass: 109277.031 Da / Num. of mol.: 1 / Fragment: UNP residues 4370-5300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: rep, 1a-1b / Plasmid: pFastBac / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0C6X7
|#2: Protein|| |
Mass: 21887.990 Da / Num. of mol.: 1 / Fragment: UNP residues 3920-4117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: 1a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Rosetta2 pLysS / References: UniProt: P0C6U8
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors|
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
|Molecular weight||Value: 0.13 MDa / Experimental value: NO|
|Source (natural)||Organism: SARS coronavirus|
|Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21 / Plasmid: pFastBac|
|Buffer solution||pH: 7.4 |
Details: n-dodecyl-beta-D-maltopyranoside was added just prior to spotting samples onto holey EM grids.
|Specimen||Conc.: 3.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 43478 X / Calibrated defocus min: 400 nm / Calibrated defocus max: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 11.75 sec. / Electron dose: 50.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1677|
|Image scans||Width: 3838 / Height: 3710 / Movie frames/image: 47 / Used frames/image: 1-47|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 2003890|
|Symmetry||Point symmetry: C1 (asymmetric)|
|3D reconstruction||Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71262 / Symmetry type: POINT|
|Atomic model building||Space: REAL|
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.:Changes in new EM Navigator and Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi