+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30226 | |||||||||
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Title | Structure of the RNA-dependent RNA polymerase from SARS-CoV-2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Polymerase / cryo-EM / REPLICATION | |||||||||
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 | SARS coronavirus / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Peng Q / Peng R | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2. Authors: Qi Peng / Ruchao Peng / Bin Yuan / Jingru Zhao / Min Wang / Xixi Wang / Qian Wang / Yan Sun / Zheng Fan / Jianxun Qi / George F Gao / Yi Shi / Abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). ...The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). The viral polymerase is a promising antiviral target. Here, we describe the near-atomic-resolution structure of the SARS-CoV-2 polymerase complex consisting of the nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases and suggests a mechanism of activation by cofactors. Biochemical studies reveal reduced activity of the core polymerase complex and lower thermostability of individual subunits of SARS-CoV-2 compared with SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate adaptation of SARS-CoV-2 toward humans with a relatively lower body temperature than the natural bat hosts. | |||||||||
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_30226.map.gz | 5.4 MB | EMDB map data format | |
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Header (meta data) | emd-30226-v30.xml emd-30226.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30226_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_30226.png | 71.5 KB | ||
Filedesc metadata | emd-30226.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30226 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30226 | HTTPS FTP |
-Validation report
Summary document | emd_30226_validation.pdf.gz | 387.9 KB | Display | EMDB validaton report |
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Full document | emd_30226_full_validation.pdf.gz | 387.5 KB | Display | |
Data in XML | emd_30226_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_30226_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30226 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30226 | HTTPS FTP |
-Related structure data
Related structure data | 7bw4MC 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_30226.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8 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 : The complex of nsp12 bound to nsp7 and nsp8
Entire | Name: The complex of nsp12 bound to nsp7 and nsp8 |
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Components |
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-Supramolecule #1: The complex of nsp12 bound to nsp7 and nsp8
Supramolecule | Name: The complex of nsp12 bound to nsp7 and nsp8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: SARS coronavirus |
-Macromolecule #1: RNA-directed RNA polymerase
Macromolecule | Name: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 105.847 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: RVCGVSAARL TPCGTGTSTD VVYRAFDIYN DKVAGFAKFL KTNCCRFQEK DEDDNLIDSY FVVKRHTFSN YQHEETIYNL LKDCPAVAK HDFFKFRIDG DMVPHISRQR LTKYTMADLV YALRHFDEGN CDTLKEILVT YNCCDDDYFN KKDWYDFVEN P DILRVYAN ...String: RVCGVSAARL TPCGTGTSTD VVYRAFDIYN DKVAGFAKFL KTNCCRFQEK DEDDNLIDSY FVVKRHTFSN YQHEETIYNL LKDCPAVAK HDFFKFRIDG DMVPHISRQR LTKYTMADLV YALRHFDEGN CDTLKEILVT YNCCDDDYFN KKDWYDFVEN P DILRVYAN LGERVRQALL KTVQFCDAMR NAGIVGVLTL DNQDLNGNWY DFGDFIQTTP GSGVPVVDSY YSLLMPILTL TR ALTAESH VDTDLTKPYI KWDLLKYDFT EERLKLFDRY FKYWDQTYHP NCVNCLDDRC ILHCANFNVL FSTVFPPTSF GPL VRKIFV DGVPFVVSTG YHFRELGVVH NQDVNLHSSR LSFKELLVYA ADPAMHAASG NLLLDKRTTC FSVAALTNNV AFQT VKPGN FNKDFYDFAV SKGFFKEGSS VELKHFFFAQ DGNAAISDYD YYRYNLPTMC DIRQLLFVVE VVDKYFDCYD GGCIN ANQV IVNNLDKSAG FPFNKWGKAR LYYDSMSYED QDALFAYTKR NVIPTITQMN LKYAISAKNR ARTVAGVSIC STMTNR QFH QKLLKSIAAT RGATVVIGTS KFYGGWHNML KTVYSDVENP HLMGWDYPKC DRAMPNMLRI MASLVLARKH TTCCSLS HR FYRLANECAQ VLSEMVMCGG SLYVKPGGTS SGDATTAYAN SVFNICQAVT ANVNALLSTD GNKIADKYVR NLQHRLYE C LYRNRDVDTD FVNEFYAYLR KHFSMMILSD DAVVCFNSTY ASQGLVASIK NFKSVLYYQN NVFMSEAKCW TETDLTKGP HEFCSQHTML VKQGDDYVYL PYPDPSRILG AGCFVDDIVK TDGTLMIERF VSLAIDAYPL TKHPNQEYAD VFHLYLQYIR KLHDELTGH MLDMYSVMLT NDNTSRYWEP EFYEAMYTPH TVLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: Non-structural protein 8
Macromolecule | Name: Non-structural protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 21.903047 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AIASEFSSLP SYAAFATAQE AYEQAVANGD SEVVLKKLKK SLNVAKSEFD RDAAMQRKLE KMADQAMTQM YKQARSEDKR AKVTSAMQT MLFTMLRKLD NDALNNIINN ARDGCVPLNI IPLTTAAKLM VVIPDYNTYK NTCDGTTFTY ASALWEIQQV V DADSKIVQ ...String: AIASEFSSLP SYAAFATAQE AYEQAVANGD SEVVLKKLKK SLNVAKSEFD RDAAMQRKLE KMADQAMTQM YKQARSEDKR AKVTSAMQT MLFTMLRKLD NDALNNIINN ARDGCVPLNI IPLTTAAKLM VVIPDYNTYK NTCDGTTFTY ASALWEIQQV V DADSKIVQ LSEISMDNSP NLAWPLIVTA LRANSAVKLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #3: Non-structural protein 7
Macromolecule | Name: Non-structural protein 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 9.248804 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SKMSDVKCTS VVLLSVLQQL RVESSSKLWA QCVQLHNDIL LAKDTTEAFE KMVSLLSVLL SMQGAVDINK LCEEMLDNRA TLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |