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Yorodumi- EMDB-26641: SARS-CoV-2 replication-transcription complex bound to ATP, in a p... -
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-Basic information
Entry | Database: EMDB / ID: EMD-26641 | |||||||||
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Title | SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state | |||||||||
Map data | SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state | |||||||||
Sample |
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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 | Severe acute respiratory syndrome coronavirus 2 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Malone BF / Perry JK / Appleby TC / Feng JY / Campbell EA / Darst SA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis for substrate selection by the SARS-CoV-2 replicase. Authors: Brandon F Malone / Jason K Perry / Paul Dominic B Olinares / Hery W Lee / James Chen / Todd C Appleby / Joy Y Feng / John P Bilello / Honkit Ng / Johanna Sotiris / Mark Ebrahim / Eugene Y D ...Authors: Brandon F Malone / Jason K Perry / Paul Dominic B Olinares / Hery W Lee / James Chen / Todd C Appleby / Joy Y Feng / John P Bilello / Honkit Ng / Johanna Sotiris / Mark Ebrahim / Eugene Y D Chua / Joshua H Mendez / Ed T Eng / Robert Landick / Matthias Götte / Brian T Chait / Elizabeth A Campbell / Seth A Darst / Abstract: The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC). Accordingly, the RTC is a target for ...The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC). Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogues, including remdesivir. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogues must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogues compete, has not been discerned in detail. Here, we use cryogenic-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart adenosine triphosphate. Our results explain the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase), an enigmatic catalytic domain essential for viral propagation. The NiRAN selectively binds guanosine triphosphate, strengthening proposals for the role of this domain in the formation of the 5' RNA cap. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26641.map.gz | 108.4 MB | EMDB map data format | |
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Header (meta data) | emd-26641-v30.xml emd-26641.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26641_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_26641.png | 38.7 KB | ||
Others | emd_26641_additional_1.map.gz emd_26641_half_map_1.map.gz emd_26641_half_map_2.map.gz | 2.4 MB 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26641 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26641 | HTTPS FTP |
-Related structure data
Related structure data | 7uo7MC 7uo4C 7uo9C 7uobC 7uoeC 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_26641.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local resolution filtered map
File | emd_26641_additional_1.map | ||||||||||||
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Annotation | Local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 replication-transcription complex bound to ATP, in a...
File | emd_26641_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 replication-transcription complex bound to ATP, in a...
File | emd_26641_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to ATP, in a pre-catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 replication-transcription complex + ATP
Entire | Name: SARS-CoV-2 replication-transcription complex + ATP |
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Components |
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-Supramolecule #1: SARS-CoV-2 replication-transcription complex + ATP
Supramolecule | Name: SARS-CoV-2 replication-transcription complex + ATP / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5 |
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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: Escherichia coli BL21(DE3) (bacteria) |
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 |
-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 BL21(DE3) (bacteria) |
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 |
-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: 10.250025 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: VACTKEVHMS KMSDVKCTSV VLLSVLQQLR VESSSKLWAQ CVQLHNDILL AKDTTEAFEK MVSLLSVLLS MQGAVDINKL CEEMLDNRA TLQ |
-Macromolecule #4: Product RNA (35-MER)
Macromolecule | Name: Product RNA (35-MER) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 11.157644 KDa |
Sequence | String: CGCGUAGCAU GCUACGUCAU UCUCCUAAGA AGCUG |
-Macromolecule #5: Template RNA (55-MER)
Macromolecule | Name: Template RNA (55-MER) / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.641477 KDa |
Sequence | String: CUAUCCCCAU GUGAGCGGCU CAGCUUCUUA GGAGAAUGAC GUAGCAUGCU ACGCG |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / 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: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.58 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |