+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24102 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / exoribonuclease / mismatch correction / VIRAL PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Liu C / Yang Y | |||||||||
Citation | Journal: Science / Year: 2021 Title: Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Authors: Chang Liu / Wei Shi / Scott T Becker / David G Schatz / Bin Liu / Yang Yang / Abstract: Coronavirus 3′-to-5′ exoribonuclease (ExoN), residing in the nonstructural protein (nsp) 10–nsp14 complex, boosts replication fidelity by proofreading RNA synthesis and is critical for the ...Coronavirus 3′-to-5′ exoribonuclease (ExoN), residing in the nonstructural protein (nsp) 10–nsp14 complex, boosts replication fidelity by proofreading RNA synthesis and is critical for the virus life cycle. ExoN also recognizes and excises nucleotide analog inhibitors incorporated into the nascent RNA, undermining the effectiveness of nucleotide analog–based antivirals. Here we present cryo–electron microscopy structures of both wild-type and mutant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp10-nsp14 in complex with an RNA substrate bearing a 3′-end mismatch at resolutions ranging from 2.5 to 3.9 angstroms. The structures reveal the molecular determinants of ExoN substrate specificity and offer insight into the molecular mechanisms of mismatch correction during coronavirus RNA synthesis. Our findings provide guidance for rational design of improved anticoronavirus therapies. | |||||||||
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_24102.map.gz | 36.2 MB | EMDB map data format | |
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Header (meta data) | emd-24102-v30.xml emd-24102.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_24102.png | 101.2 KB | ||
Filedesc metadata | emd-24102.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24102 | HTTPS FTP |
-Validation report
Summary document | emd_24102_validation.pdf.gz | 459.6 KB | Display | EMDB validaton report |
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Full document | emd_24102_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | emd_24102_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_24102_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24102 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24102 | HTTPS FTP |
-Related structure data
Related structure data | 7n0bMC 7n0cC 7n0dC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24102.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.068 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 nsp10-nsp14 (WT)-RNA complex
Entire | Name: SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex |
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Components |
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-Supramolecule #1: SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex
Supramolecule | Name: SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Non-structural protein 10
Macromolecule | Name: Non-structural protein 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 14.80293 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AGNATEVPAN STVLSFCAFA VDAAKAYKDY LASGGQPITN CVKMLCTHTG TGQAITVTPE ANMDQESFGG ASCCLYCRCH IDHPNPKGF CDLKGKYVQI PTTCANDPVG FTLKNTVCTV CGMWKGYGCS CDQLREPMLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: Proofreading exoribonuclease
Macromolecule | Name: Proofreading exoribonuclease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 59.88748 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AENVTGLFKD CSKVITGLHP TQAPTHLSVD TKFKTEGLCV DIPGIPKDMT YRRLISMMGF KMNYQVNGYP NMFITREEAI RHVRAWIGF DVEGCHATRE AVGTNLPLQL GFSTGVNLVA VPTGYVDTPN NTDFSRVSAK PPPGDQFKHL IPLMYKGLPW N VVRIKIVQ ...String: AENVTGLFKD CSKVITGLHP TQAPTHLSVD TKFKTEGLCV DIPGIPKDMT YRRLISMMGF KMNYQVNGYP NMFITREEAI RHVRAWIGF DVEGCHATRE AVGTNLPLQL GFSTGVNLVA VPTGYVDTPN NTDFSRVSAK PPPGDQFKHL IPLMYKGLPW N VVRIKIVQ MLSDTLKNLS DRVVFVLWAH GFELTSMKYF VKIGPERTCC LCDRRATCFS TASDTYACWH HSIGFDYVYN PF MIDVQQW GFTGNLQSNH DLYCQVHGNA HVASCDAIMT RCLAVHECFV KRVDWTIEYP IIGDELKINA ACRKVQHMVV KAA LLADKF PVLHDIGNPK AIKCVPQADV EWKFYDAQPC SDKAYKIEEL FYSYATHSDK FTDGVCLFWN CNVDRYPANS IVCR FDTRV LSNLNLPGCD GGSLYVNKHA FHTPAFDKSA FVNLKQLPFF YYSDSPCESH GKQVVSDIDY VPLKSATCIT RCNLG GAVC RHHANEYRLY LDAYNMMISA GFSLWVYKQF DTYNLWNTFT RLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #3: RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*...
Macromolecule | Name: RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 12.246229 KDa |
Sequence | String: GGGGAUGUGA UUUUAAUAGC UUCUUAGGAG AAUGACUU |
-Macromolecule #4: RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*...
Macromolecule | Name: RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 10.459259 KDa |
Sequence | String: CGGUCAUUCU CCUAAGAAGC UAUUAAAAUC ACC |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 BIOQUANTUM (6k x 4k) / Average electron dose: 49.49 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82543 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |