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- EMDB-42488: Porcine epidemic diarrhea virus complete core polymerase complex -

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Entry
Database: EMDB / ID: EMD-42488
TitlePorcine epidemic diarrhea virus complete core polymerase complex
Map dataSingle particle reconstruction of PEDV core polymerase complex
Sample
  • Complex: Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short RNA substrate
    • Protein or peptide: nsp12
    • Protein or peptide: nsp8
    • Protein or peptide: nsp7
    • RNA: RNA (33-MER)
    • RNA: RNA (55-MER)
  • Ligand: ZINC ION
KeywordsCoronavirus / nsp12 / RNA polymerase / PEDV / REPLICATION / TRANSFERASE-RNA complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity ...host cell membrane / viral genome replication / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / 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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAnderson TK / Kirchdoerfer RN
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158463 United States
United States Department of Agriculture (USDA)WIS03099 United States
CitationJournal: bioRxiv / Year: 2023
Title: An alphacoronavirus polymerase structure reveals conserved co-factor functions.
Authors: Thomas K Anderson / Peter J Hoferle / Kenneth W Lee / Joshua J Coon / Robert N Kirchdoerfer /
Abstract: Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral ...Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for RNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.
History
DepositionOct 25, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42488.png

Downloads & links

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Map

FileDownload / File: emd_42488.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle reconstruction of PEDV core polymerase complex
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.179
Minimum - Maximum-1.3564203 - 2.2126753
Average (Standard dev.)0.0020907542 (±0.04851536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42488_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_42488_half_map_1.map
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Histogram

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Half map: #1

Fileemd_42488_half_map_2.map
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Sample components

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Entire : Core polymerase complex of the porcine epidemic diarrhea virus co...

EntireName: Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short RNA substrate
Components
  • Complex: Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short RNA substrate
    • Protein or peptide: nsp12
    • Protein or peptide: nsp8
    • Protein or peptide: nsp7
    • RNA: RNA (33-MER)
    • RNA: RNA (55-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Core polymerase complex of the porcine epidemic diarrhea virus co...

SupramoleculeName: Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short RNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 185 KDa

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Macromolecule #1: nsp12

MacromoleculeName: nsp12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 108.994758 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: STDMAYLNRV RGSSAARLEP CNGTDTQHVY RAFDIYNKDV ACLGKFLKVN CVRLKNLDKH DAFYVVKRCT KSAMEHEQSI YSRLEKCGA VAEHDFFTWK DGRAIYGNVC RKDLTEYTMM DLCYALRNFD ENNCDVLKSI LIKVGACEES YFNNKVWFDP V ENEDIHRV ...String:
STDMAYLNRV RGSSAARLEP CNGTDTQHVY RAFDIYNKDV ACLGKFLKVN CVRLKNLDKH DAFYVVKRCT KSAMEHEQSI YSRLEKCGA VAEHDFFTWK DGRAIYGNVC RKDLTEYTMM DLCYALRNFD ENNCDVLKSI LIKVGACEES YFNNKVWFDP V ENEDIHRV YALLGTIVSR AMLKCVKFCD AMVEQGIVGV VTLDNQDLNG DFYDFGDFTC SIKGMGIPIC TSYYSYMMPV MG MTNCLAS ECFVKSDIFG EDFKSYDLLE YDFTEHKTAL FNKYFKYWGL QYHPNCVDCS DEQCIVHCAN FNTLFSTTIP ITA FGPLCR KCWIDGVPLV TTAGYHFKQL GIVWNNDLNL HSSRLSINEL LQFCSDPALL IASSPALVDQ RTVCFSVAAL GTGM TNQTV KPGHFNKEFY DFLLEQGFFS EGSELTLKHF FFAQKGDAAV KDFDYYRYNR PTVLDICQAR VVYQIVQRYF DIYEG GCIT AKEVVVTNLN KSAGYPLNKF GKAGLYYESL SYEEQDELYA YTKRNILPTM TQLNLKYAIS GKERARTVGG VSLLST MTT RQYHQKHLKS IVNTRGASVV IGTTKFYGGW DNMLKNLIDG VENPCLMGWD YPKCDRALPN MIRMISAMIL GSKHTTC CS STDRFFRLCN ELAQVLTEVV YSNGGFYLKP GGTTSGDATT AYANSVFNIF QAVSANVNKL LSVDSNVCHN LEVKQLQR K LYECCYRSTT VDDQFVVEYY GYLRKHFSMM ILSDDGVVCY NNDYASLGYV ADLNAFKAVL YYQNNVFMSA SKCWIEPDI NKGPHEFCSQ HTMQIVDKDG TYYLPYPDPS RILSAGVFVD DVVKTDAVVL LERYVSLAID AYPLSKHENP EYKKVFYVLL DWVKHLYKT LNAGVLESFS VTLLEDSTAK FWDESFYANM YEKSAVLQEN LYFQGSWSHP QFEKGGSGSS WSHPQFEK

UniProtKB: ORF1ab polyprotein

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Macromolecule #2: nsp8

MacromoleculeName: nsp8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 21.716838 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SVASTYVGLP SYVIYENARQ QYEDAVNNGS PPQLVKQLRH AMNVAKSEFD REASTQRKLD RMAEQAAAQM YKEARAVNRK SKVVSAMHS LLFGMLRRLD MSSVDTILNL AKDGVVPLSV IPAVSATKLN IVTSDIDSYN RIQREGCVHY AGTIWNIIDI K DNDGKVVH ...String:
SVASTYVGLP SYVIYENARQ QYEDAVNNGS PPQLVKQLRH AMNVAKSEFD REASTQRKLD RMAEQAAAQM YKEARAVNRK SKVVSAMHS LLFGMLRRLD MSSVDTILNL AKDGVVPLSV IPAVSATKLN IVTSDIDSYN RIQREGCVHY AGTIWNIIDI K DNDGKVVH VKEVTAQNAE SLSWPLVLGC ERIVKLQ

UniProtKB: ORF1ab polyprotein

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Macromolecule #3: nsp7

MacromoleculeName: nsp7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 9.230511 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SKLTDIKCSN VVLLGCLSSM NVSANSTEWA YCVDLHNKIN LCNDPEKAQE MLLALLAFFL SKNSAFGLDD LLESYFNDNS MLQ

UniProtKB: ORF1ab polyprotein

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Macromolecule #4: RNA (33-MER)

MacromoleculeName: RNA (33-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.468266 KDa
SequenceString:
CAUUCUCCUA AGAAGCUAUU AAAAUCACAG AUU

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Macromolecule #5: RNA (55-MER)

MacromoleculeName: RNA (55-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.740572 KDa
SequenceString:
CAGUGUCAUG GAAAAACAGA AAAAUCUGUG AUUUUAAUAG CUUCUUAGGA GAAUG

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
25.0 mMHEPES
2.0 mMMgCl2Magnesium Chloride
2.0 mMdithiothreitol
6.0 mMCHAPSO
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7krp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.0) / Number images used: 103940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.0)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.1.0)
FSC plot (resolution estimation)

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