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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23109 | |||||||||
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Title | SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate | |||||||||
![]() | SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate | |||||||||
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Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bravo JPK / Taylor DW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Authors: Jack P K Bravo / Tyler L Dangerfield / David W Taylor / Kenneth A Johnson / ![]() Abstract: Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase ...Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 126.4 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l1fMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : SARS-CoV-2 RdRp complex with template:primer and four RMP
Entire | Name: SARS-CoV-2 RdRp complex with template:primer and four RMP |
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Components |
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-Supramolecule #1: SARS-CoV-2 RdRp complex with template:primer and four RMP
Supramolecule | Name: SARS-CoV-2 RdRp complex with template:primer and four RMP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: RNA-directed RNA polymerase, Non-structural protein 8, Non-struct...
Supramolecule | Name: RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 |
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-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: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 103.372164 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: YRAFDIYNDK VAGFAKFLKT NCCRFQEKDE DDNLIDSYFV VKRHTFSNYQ HEETIYNLLK DCPAVAKHDF FKFRIDGDMV PHISRQRLT KYTMADLVYA LRHFDEGNCD TLKEILVTYN CCDDDYFNKK DWYDFVENPD ILRVYANLGE RVRQALLKTV Q FCDAMRNA ...String: YRAFDIYNDK VAGFAKFLKT NCCRFQEKDE DDNLIDSYFV VKRHTFSNYQ HEETIYNLLK DCPAVAKHDF FKFRIDGDMV PHISRQRLT KYTMADLVYA LRHFDEGNCD TLKEILVTYN CCDDDYFNKK DWYDFVENPD ILRVYANLGE RVRQALLKTV Q FCDAMRNA GIVGVLTLDN QDLNGNWYDF GDFIQTTPGS GVPVVDSYYS LLMPILTLTR ALTAESHVDT DLTKPYIKWD LL KYDFTEE RLKLFDRYFK YWDQTYHPNC VNCLDDRCIL HCANFNVLFS TVFPPTSFGP LVRKIFVDGV PFVVSTGYHF REL GVVHNQ DVNLHSSRLS FKELLVYAAD PAMHAASGNL LLDKRTTCFS VAALTNNVAF QTVKPGNFNK DFYDFAVSKG FFKE GSSVE LKHFFFAQDG NAAISDYDYY RYNLPTMCDI RQLLFVVEVV DKYFDCYDGG CINANQVIVN NLDKSAGFPF NKWGK ARLY YDSMSYEDQD ALFAYTKRNV IPTITQMNLK YAISAKNRAR TVAGVSICST MTNRQFHQKL LKSIAATRGA TVVIGT SKF YGGWHNMLKT VYSDVENPHL MGWDYPKCDR AMPNMLRIMA SLVLARKHTT CCSLSHRFYR LANECAQVLS EMVMCGG SL YVKPGGTSSG DATTAYANSV FNICQAVTAN VNALLSTDGN KIADKYVRNL QHRLYECLYR NRDVDTDFVN EFYAYLRK H FSMMILSDDA VVCFNSTYAS QGLVASIKNF KSVLYYQNNV FMSEAKCWTE TDLTKGPHEF CSQHTMLVKQ GDDYVYLPY PDPSRILGAG CFVDDIVKTD GTLMIERFVS LAIDAYPLTK HPNQEYADVF HLYLQYIRKL HDELTGHMLD MYSVMLTNDN TSRYWEPEF YEAMYTPHT 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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 12.644559 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: DKRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT YKNTCDGTTF TYASALWEIQ QVVDADSKI VQLSEISMDN SPNLAWPLIV TALRA 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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 7.001255 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: KMSDVKCTSV VLLSVLQQLR VESSSKLWAQ CVQLHNDILL AKDTTEAFEK MVSLLSVLLS MQG UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #4: RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F8...
Macromolecule | Name: RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F86)*(F86))-3') type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 5.539421 KDa |
Sequence | String: CUAAGAAGCU AUU(F86)(F86)(F86)(F86) |
-Macromolecule #5: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')
Macromolecule | Name: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3') type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 5.657339 KDa |
Sequence | String: AUUUUAAUAG CUUCUUAG |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116748 |