[English] 日本語
Yorodumi
- PDB-6nur: SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nur
TitleSARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors
Components
  • NSP12
  • NSP7
  • NSP8
KeywordsVIRAL 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
nsp7 replicase / Macro domain / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / RNA synthesis protein NSP10, coronavirus / (+) RNA virus helicase core domain / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus ...nsp7 replicase / Macro domain / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / RNA synthesis protein NSP10, coronavirus / (+) RNA virus helicase core domain / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP1, betacoronavirus / RNA-directed RNA polymerase, catalytic domain / RNA synthesis protein NSP10 superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase S1, PA clan / Non-structural protein NSP16, coronavirus-like / Non-structural protein NSP11, coronavirus / RNA polymerase, N-terminal, coronaviral / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / in:ipr014827: / Non-structural protein NSP7, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Coronaviridae zinc-binding domain / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus RPol N-terminus / nsp8 replicase / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus
Replicase polyprotein 1a / Replicase polyprotein 1ab
Biological speciesHuman SARS coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKirchdoerfer, R.N. / Ward, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127521 United States
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0520
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NSP12
B: NSP8
C: NSP7
D: NSP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5186
Polymers162,3874
Non-polymers1312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9380 Å2
ΔGint-91 kcal/mol
Surface area44480 Å2

-
Components

#1: Protein NSP12


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 NSP8


Mass: 21887.990 Da / Num. of mol.: 2 / Fragment: UNP residues 3920-4117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: 1a / Plasmid: pET46 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Rosetta2 pLysS / References: UniProt: P0C6U8
#3: Protein NSP7


Mass: 9333.869 Da / Num. of mol.: 1 / Fragment: UNP residues 3837-3919
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: rep, 1a-1b / Plasmid: pET46 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Rosetta2 pLysS / References: UniProt: P0C6X7
#4: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: NO
Source (natural)Organism: SARS coronavirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21 / Plasmid: pFastBac
Buffer solutionpH: 7.4
Details: n-dodecyl-beta-D-maltopyranoside was added just prior to spotting samples onto holey EM grids.
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2300 mMsodium chlorideNaClSodium chloride1
32 mMTCEP1
40.010 mMmagnesium chlorideMgCl21
50.060 mMn-dodecyl-beta-D-maltopyranoside1
SpecimenConc.: 3.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansWidth: 3838 / Height: 3710 / Movie frames/image: 47 / Used frames/image: 1-47

-
Processing

EM software
IDNameVersionCategory
1DoG Pickerparticle selection
2Leginonimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9Rosetta3.1model refinement
10PHENIX1.14rc3-3199model refinement
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2003890
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71046 / Symmetry type: POINT
Atomic model buildingSpace: REAL

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

-
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

External links:EMDB at PDBe / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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

Read more

-
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

Read more