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Yorodumi- EMDB-34370: Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34370 | ||||||||||||
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Title | Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypol binding | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | SARS-CoV-2 / RdRp / Inhibitor / VIRAL PROTEIN | ||||||||||||
Function / homology | Function and homology information viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / methylation / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 | electron tomography / cryo EM | ||||||||||||
Authors | Wang W / Ren M / Li F | ||||||||||||
Funding support | 3 items
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Citation | Journal: To Be Published Title: Structure of SARS-CoV-2 RNA-dependent RNA polymerase with gossypol binding Authors: Wang W / Li W / Ren M / Li F | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34370.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-34370-v30.xml emd-34370.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_34370.png | 93.5 KB | ||
Filedesc metadata | emd-34370.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34370 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34370 | HTTPS FTP |
-Validation report
Summary document | emd_34370_validation.pdf.gz | 311.6 KB | Display | EMDB validaton report |
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Full document | emd_34370_full_validation.pdf.gz | 311.1 KB | Display | |
Data in XML | emd_34370_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_34370_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34370 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34370 | HTTPS FTP |
-Related structure data
Related structure data | 8gy6MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34370.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Nsp12-Nsp7-Nsp8 complex bound to gossypol
Entire | Name: SARS-CoV-2 Nsp12-Nsp7-Nsp8 complex bound to gossypol |
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Components |
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-Supramolecule #1: SARS-CoV-2 Nsp12-Nsp7-Nsp8 complex bound to gossypol
Supramolecule | Name: SARS-CoV-2 Nsp12-Nsp7-Nsp8 complex bound to gossypol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-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: 106.780977 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN ...String: SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN PDILRVYANL GERVRQALLK TVQFCDAMRN AGIVGVLTLD NQDLNGNWYD FGDFIQTTPG SGVPVVDSYY SL LMPILTL TRALTAESHV DTDLTKPYIK WDLLKYDFTE ERLKLFDRYF KYWDQTYHPN CVNCLDDRCI LHCANFNVLF STV FPPTSF GPLVRKIFVD GVPFVVSTGY HFRELGVVHN QDVNLHSSRL SFKELLVYAA DPAMHAASGN LLLDKRTTCF SVAA LTNNV AFQTVKPGNF NKDFYDFAVS KGFFKEGSSV ELKHFFFAQD GNAAISDYDY YRYNLPTMCD IRQLLFVVEV VDKYF DCYD GGCINANQVI VNNLDKSAGF PFNKWGKARL YYDSMSYEDQ DALFAYTKRN VIPTITQMNL KYAISAKNRA RTVAGV SIC STMTNRQFHQ KLLKSIAATR GATVVIGTSK FYGGWHNMLK TVYSDVENPH LMGWDYPKCD RAMPNMLRIM ASLVLAR KH TTCCSLSHRF YRLANECAQV LSEMVMCGGS LYVKPGGTSS GDATTAYANS VFNICQAVTA NVNALLSTDG NKIADKYV R NLQHRLYECL YRNRDVDTDF VNEFYAYLRK HFSMMILSDD AVVCFNSTYA SQGLVASIKN FKSVLYYQNN VFMSEAKCW TETDLTKGPH EFCSQHTMLV KQGDDYVYLP YPDPSRILGA GCFVDDIVKT DGTLMIERFV SLAIDAYPLT KHPNQEYADV FHLYLQYIR KLHDELTGHM LDMYSVMLTN DNTSRYWEPE FYEAMYTPHT VLQ 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: Spodoptera frugiperda (fall armyworm) |
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: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SKMSDVKCTS VVLLSVLQQL RVESSSKLWA QCVQLHNDIL LAKDTTEAFE KMVSLLSVLL SMQGAVDINK LCEEMLDNRA TLQ UniProtKB: Replicase polyprotein 1a |
-Macromolecule #4: Gossypol
Macromolecule | Name: Gossypol / type: ligand / ID: 4 / Number of copies: 2 / Formula: GO3 |
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Molecular weight | Theoretical: 518.554 Da |
Chemical component information | ChemComp-GO3: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
-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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 1224147 |
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