+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30209 | |||||||||
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Title | Cryo-EM structure of the apo nsp12-nsp7-nsp8 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / RNA Polymerase / Apo / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 bat coronavirus / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Yin W / Mao C | |||||||||
Citation | Journal: Science / Year: 2020 Title: Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Authors: Wanchao Yin / Chunyou Mao / Xiaodong Luan / Dan-Dan Shen / Qingya Shen / Haixia Su / Xiaoxi Wang / Fulai Zhou / Wenfeng Zhao / Minqi Gao / Shenghai Chang / Yuan-Chao Xie / Guanghui Tian / He- ...Authors: Wanchao Yin / Chunyou Mao / Xiaodong Luan / Dan-Dan Shen / Qingya Shen / Haixia Su / Xiaoxi Wang / Fulai Zhou / Wenfeng Zhao / Minqi Gao / Shenghai Chang / Yuan-Chao Xie / Guanghui Tian / He-Wei Jiang / Sheng-Ce Tao / Jingshan Shen / Yi Jiang / Hualiang Jiang / Yechun Xu / Shuyang Zhang / Yan Zhang / H Eric Xu / Abstract: The pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS-CoV-2 requires the viral ...The pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS-CoV-2 requires the viral RNA-dependent RNA polymerase (RdRp) enzyme, a target of the antiviral drug remdesivir. Here we report the cryo-electron microscopy structure of the SARS-CoV-2 RdRp, both in the apo form at 2.8-angstrom resolution and in complex with a 50-base template-primer RNA and remdesivir at 2.5-angstrom resolution. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp, where remdesivir is covalently incorporated into the primer strand at the first replicated base pair, and terminates chain elongation. Our structures provide insights into the mechanism of viral RNA replication and a rational template for drug design to combat the viral infection. | |||||||||
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_30209.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-30209-v30.xml emd-30209.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_30209.png | 64.2 KB | ||
Filedesc metadata | emd-30209.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30209 | HTTPS FTP |
-Related structure data
Related structure data | 7bv1MC 7bv2C 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_30209.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.014 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 apo nsp12-nsp7-nsp8 complex
Entire | Name: the apo nsp12-nsp7-nsp8 complex |
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Components |
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-Supramolecule #1: the apo nsp12-nsp7-nsp8 complex
Supramolecule | Name: the apo nsp12-nsp7-nsp8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: SARS bat 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: 109.070445 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSADAQSFLN RVCGVSAARL TPCGTGTSTD VVYRAFDIYN DKVAGFAKFL KTNCCRFQEK DEDDNLIDSY FVVKRHTFSN YQHEETIYN LLKDCPAVAK HDFFKFRIDG DMVPHISRQR LTKYTMADLV YALRHFDEGN CDTLKEILVT YNCCDDDYFN K KDWYDFVE ...String: MSADAQSFLN RVCGVSAARL TPCGTGTSTD VVYRAFDIYN DKVAGFAKFL KTNCCRFQEK DEDDNLIDSY FVVKRHTFSN YQHEETIYN LLKDCPAVAK HDFFKFRIDG DMVPHISRQR LTKYTMADLV YALRHFDEGN CDTLKEILVT YNCCDDDYFN K KDWYDFVE NPDILRVYAN LGERVRQALL KTVQFCDAMR NAGIVGVLTL DNQDLNGNWY DFGDFIQTTP GSGVPVVDSY YS LLMPILT LTRALTAESH VDTDLTKPYI KWDLLKYDFT EERLKLFDRY FKYWDQTYHP NCVNCLDDRC ILHCANFNVL FST VFPPTS FGPLVRKIFV DGVPFVVSTG YHFRELGVVH NQDVNLHSSR LSFKELLVYA ADPAMHAASG NLLLDKRTTC FSVA ALTNN VAFQTVKPGN FNKDFYDFAV SKGFFKEGSS VELKHFFFAQ DGNAAISDYD YYRYNLPTMC DIRQLLFVVE VVDKY FDCY DGGCINANQV IVNNLDKSAG FPFNKWGKAR LYYDSMSYED QDALFAYTKR NVIPTITQMN LKYAISAKNR ARTVAG VSI CSTMTNRQFH QKLLKSIAAT RGATVVIGTS KFYGGWHNML KTVYSDVENP HLMGWDYPKC DRAMPNMLRI MASLVLA RK HTTCCSLSHR FYRLANECAQ VLSEMVMCGG SLYVKPGGTS SGDATTAYAN SVFNICQAVT ANVNALLSTD GNKIADKY V RNLQHRLYEC LYRNRDVDTD FVNEFYAYLR KHFSMMILSD DAVVCFNSTY ASQGLVASIK NFKSVLYYQN NVFMSEAKC WTETDLTKGP HEFCSQHTML VKQGDDYVYL PYPDPSRILG AGCFVDDIVK TDGTLMIERF VSLAIDAYPL TKHPNQEYAD VFHLYLQYI RKLHDELTGH MLDMYSVMLT NDNTSRYWEP EFYEAMYTPH TVLQGGSENL YFQGHHHHHH HH 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: 23.139418 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAIASEFSSL PSYAAFATAQ EAYEQAVANG DSEVVLKKLK KSLNVAKSEF DRDAAMQRKL EKMADQAMTQ MYKQARSEDK RAKVTSAMQ TMLFTMLRKL DNDALNNIIN NARDGCVPLN IIPLTTAAKL MVVIPDYNTY KNTCDGTTFT YASALWEIQQ V VDADSKIV ...String: MAIASEFSSL PSYAAFATAQ EAYEQAVANG DSEVVLKKLK KSLNVAKSEF DRDAAMQRKL EKMADQAMTQ MYKQARSEDK RAKVTSAMQ TMLFTMLRKL DNDALNNIIN NARDGCVPLN IIPLTTAAKL MVVIPDYNTY KNTCDGTTFT YASALWEIQQ V VDADSKIV QLSEISMDNS PNLAWPLIVT ALRANSAVKL QHHHHHHHH 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: 10.485176 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSKMSDVKCT SVVLLSVLQQ LRVESSSKLW AQCVQLHNDI LLAKDTTEAF EKMVSLLSVL LSMQGAVDIN KLCEEMLDNR ATLQHHHHH HHH 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 64.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81494 |