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- EMDB-30795: Structure of COVID-19 RNA-dependent RNA polymerase (extended conf... -

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Basic information

Entry
Database: EMDB / ID: EMD-30795
TitleStructure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir
Map data
Sample
  • Complex: COVID-19 RdRp complex (exntended conformation) bound to penciclovir
    • RNA: RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
    • Protein or peptide: RNA-directed RNA polymerase
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
  • RNA: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')
  • Ligand: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: water
KeywordsCOVID-19 / RNA polymerase in extended conformation / penciclovir binding / VIRAL PROTEIN
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase 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 / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLi Z / Yu X
CitationJournal: To Be Published
Title: Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
Authors: Yin W / Luan X / Li Z / Xie Y / Zhou Z / Liu J / Gao M / Wang X / Zhou F / Wang Q / Wang Q / Shen D / Zhang Y / Tian G / Aisa H / Wei D / Jiang Y / Xiao G / Jiang H / Zhang L / Yu X / Shen J / Zhang S / Xu H
History
DepositionDec 14, 2020-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dok
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30795.png

Downloads & links

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Map

FileDownload / File: emd_30795.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.664 Å		1.07 Å/pix.
x 256 pix.
= 273.664 Å		1.07 Å/pix.
x 256 pix.
= 273.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.021
Minimum - Maximum-0.0959924 - 0.19702816
Average (Standard dev.)-0.000016453421 (±0.0061631454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.664 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0691.0691.069
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.664273.664273.664
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0960.197-0.000

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Supplemental data

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Sample components

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Entire : COVID-19 RdRp complex (exntended conformation) bound to penciclovir

EntireName: COVID-19 RdRp complex (exntended conformation) bound to penciclovir
Components
  • Complex: COVID-19 RdRp complex (exntended conformation) bound to penciclovir
    • RNA: RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
    • Protein or peptide: RNA-directed RNA polymerase
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
  • RNA: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')
  • Ligand: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: water

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Supramolecule #1: COVID-19 RdRp complex (exntended conformation) bound to penciclovir

SupramoleculeName: COVID-19 RdRp complex (exntended conformation) bound to penciclovir
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP...

MacromoleculeName: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 6.410816 KDa
SequenceString:
GCUAUGUGAG AUUAAGUUAU

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Macromolecule #2: RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP...

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 7.51851 KDa
SequenceString:
CCCUAUAACU UAAUCUCACA UAGC

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Macromolecule #3: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 107.96525 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 YFQG

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: Non-structural protein 8

MacromoleculeName: Non-structural protein 8 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.034242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 Q

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #5: Non-structural protein 7

MacromoleculeName: Non-structural protein 7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 9.38 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSKMSDVKCT SVVLLSVLQQ LRVESSSKLW AQCVQLHNDI LLAKDTTEAF EKMVSLLSVL LSMQGAVDIN KLCEEMLDNR ATLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #6: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl...

MacromoleculeName: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate
type: ligand / ID: 6 / Number of copies: 1 / Formula: HCU
Molecular weightTheoretical: 333.238 Da
Chemical component information

ChemComp-HCU:
[(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: PYROPHOSPHATE 2-

MacromoleculeName: PYROPHOSPHATE 2- / type: ligand / ID: 9 / Number of copies: 2 / Formula: POP
Molecular weightTheoretical: 175.959 Da
Chemical component information

ChemComp-POP:
PYROPHOSPHATE 2-

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139773
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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