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- EMDB-30275: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30275
TitleCOVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
Map data
Sample
  • Complex: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
    • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
    • RNA: RNA (29-MER)
    • RNA: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3')
  • Ligand: ZINC ION
KeywordsCOVID-19 / 2019-nCoV / SARS-CoV-2 / Virus / RdRp / nsp12 / nsp7 / nsp8 / RTC / cryo-EM / Viral protein / RNA polymerase / drug target / antiviral / pre-translocated catalytic complex / VIRAL PROTEIN-RNA complex
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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / TRAF3-dependent IRF activation pathway / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / 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 / ubiquitinyl hydrolase 1 / DNA helicase / 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 / identical protein binding
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Foot-and-mouth disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsWang Q / Gao Y / Ji W / Mu A / Rao Z
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
Ministry of Science and Technology (MoST, China)2020YFA0707500 China
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)32041007 China
CitationJournal: Cell / Year: 2020
Title: Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.
Authors: Quan Wang / Jiqin Wu / Haofeng Wang / Yan Gao / Qiaojie Liu / An Mu / Wenxin Ji / Liming Yan / Yan Zhu / Chen Zhu / Xiang Fang / Xiaobao Yang / Yucen Huang / Hailong Gao / Fengjiang Liu / Ji ...Authors: Quan Wang / Jiqin Wu / Haofeng Wang / Yan Gao / Qiaojie Liu / An Mu / Wenxin Ji / Liming Yan / Yan Zhu / Chen Zhu / Xiang Fang / Xiaobao Yang / Yucen Huang / Hailong Gao / Fengjiang Liu / Ji Ge / Qianqian Sun / Xiuna Yang / Wenqing Xu / Zhijie Liu / Haitao Yang / Zhiyong Lou / Biao Jiang / Luke W Guddat / Peng Gong / Zihe Rao /
Abstract: Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete ...Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete mechanistic understanding of the viral RNA-dependent RNA polymerase nsp12 drug interactions. Here, we examine the molecular basis of SARS-CoV-2 RNA replication by determining the cryo-EM structures of the stalled pre- and post- translocated polymerase complexes. Compared with the apo complex, the structures show notable structural rearrangements happening to nsp12 and its co-factors nsp7 and nsp8 to accommodate the nucleic acid, whereas there are highly conserved residues in nsp12, positioning the template and primer for an in-line attack on the incoming nucleotide. Furthermore, we investigate the inhibition mechanism of the triphosphate metabolite of remdesivir through structural and kinetic analyses. A transition model from the nsp7-nsp8 hexadecameric primase complex to the nsp12-nsp7-nsp8 polymerase complex is also proposed to provide clues for the understanding of the coronavirus transcription and replication machinery.
History
DepositionMay 7, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface level: 0.3
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  • Surface view with fitted model
  • Atomic models: PDB-7c2k
  • Surface level: 0.4
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_30275.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.7711071 - 3.3386803
Average (Standard dev.)0.0020826722 (±0.09211229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.7713.3390.002

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Supplemental data

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Mask #1

Fileemd_30275_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_30275_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_30275_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic ...

EntireName: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
Components
  • Complex: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
    • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
    • RNA: RNA (29-MER)
    • RNA: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3')
  • Ligand: ZINC ION

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Supramolecule #1: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic ...

SupramoleculeName: COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: full-length COVID-19 nsp12 (residues S1-Q932) was incubated with nsp7 (residues S1-Q83) and nsp8 (A1-Q198), and in complex with RNA template and product.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 108.350703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSADAQSFL NRVCGVSAAR LTPCGTGTST DVVYRAFDIY NDKVAGFAKF LKTNCCRFQE KDEDDNLIDS YFVVKRHTFS NYQHEETIY NLLKDCPAVA KHDFFKFRID GDMVPHISRQ RLTKYTMADL VYALRHFDEG NCDTLKEILV TYNCCDDDYF N KKDWYDFV ...String:
MGSADAQSFL NRVCGVSAAR LTPCGTGTST DVVYRAFDIY NDKVAGFAKF LKTNCCRFQE KDEDDNLIDS YFVVKRHTFS NYQHEETIY NLLKDCPAVA KHDFFKFRID GDMVPHISRQ RLTKYTMADL VYALRHFDEG NCDTLKEILV TYNCCDDDYF N KKDWYDFV ENPDILRVYA NLGERVRQAL LKTVQFCDAM RNAGIVGVLT LDNQDLNGNW YDFGDFIQTT PGSGVPVVDS YY SLLMPIL TLTRALTAES HVDTDLTKPY IKWDLLKYDF TEERLKLFDR YFKYWDQTYH PNCVNCLDDR CILHCANFNV LFS TVFPPT SFGPLVRKIF VDGVPFVVST GYHFRELGVV HNQDVNLHSS RLSFKELLVY AADPAMHAAS GNLLLDKRTT CFSV AALTN NVAFQTVKPG NFNKDFYDFA VSKGFFKEGS SVELKHFFFA QDGNAAISDY DYYRYNLPTM CDIRQLLFVV EVVDK YFDC YDGGCINANQ VIVNNLDKSA GFPFNKWGKA RLYYDSMSYE DQDALFAYTK RNVIPTITQM NLKYAISAKN RARTVA GVS ICSTMTNRQF HQKLLKSIAA TRGATVVIGT SKFYGGWHNM LKTVYSDVEN PHLMGWDYPK CDRAMPNMLR IMASLVL AR KHTTCCSLSH RFYRLANECA QVLSEMVMCG GSLYVKPGGT SSGDATTAYA NSVFNICQAV TANVNALLST DGNKIADK Y VRNLQHRLYE CLYRNRDVDT DFVNEFYAYL RKHFSMMILS DDAVVCFNST YASQGLVASI KNFKSVLYYQ NNVFMSEAK CWTETDLTKG PHEFCSQHTM LVKQGDDYVY LPYPDPSRIL GAGCFVDDIV KTDGTLMIER FVSLAIDAYP LTKHPNQEYA DVFHLYLQY IRKLHDELTG HMLDMYSVML TNDNTSRYWE PEFYEAMYTP HTVLQHHHHH HHHHH

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #2: Non-structural protein 8

MacromoleculeName: Non-structural protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.057213 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPAIASEFSS LPSYAAFATA QEAYEQAVAN GDSEVVLKKL KKSLNVAKSE FDRDAAMQRK LEKMADQAMT QMYKQARSED KRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT YKNTCDGTTF TYASALWEIQ Q VVDADSKI ...String:
GPAIASEFSS LPSYAAFATA QEAYEQAVAN GDSEVVLKKL KKSLNVAKSE FDRDAAMQRK LEKMADQAMT QMYKQARSED KRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT YKNTCDGTTF TYASALWEIQ Q VVDADSKI VQLSEISMDN SPNLAWPLIV TALRANSAVK LQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #3: Non-structural protein 7

MacromoleculeName: Non-structural protein 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 9.402971 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPSKMSDVKC TSVVLLSVLQ QLRVESSSKL WAQCVQLHND ILLAKDTTEA FEKMVSLLSV LLSMQGAVDI NKLCEEMLDN RATLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: RNA (29-MER)

MacromoleculeName: RNA (29-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 9.293521 KDa
SequenceString:
GGGAGAUGUC UCCUCCUGUG UCGUCGAAA

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Macromolecule #5: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*...

MacromoleculeName: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 5.835554 KDa
SequenceString:
UGUUCGACGA CACAGG(F86)G

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214419
Image recording ID1

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