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- EMDB-22160: Structure of SARS-CoV-2 replication-transcription complex bound t... -

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Entry
Database: EMDB / ID: EMD-22160
TitleStructure of SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
    • Protein or peptide: x 4 types
    • RNA: x 2 types
  • Ligand: x 5 types
KeywordsRNA-dependent RNA polymerase / viral replication-transcription complex / transcription / viral proteins / TRANSFERASE-HYDROLASE-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 / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 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 / : / 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 / 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.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen J / Malone B
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: bioRxiv / Year: 2020
Title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Ed Eng / Hasan Vatandaslar / Brian T Chait / Tarun Kapoor / ...Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Ed Eng / Hasan Vatandaslar / Brian T Chait / Tarun Kapoor / Seth A Darst / Elizabeth A Campbell /
Abstract: SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a ...SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.
History
DepositionJun 14, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
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  • Surface level: 0.25
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  • Atomic models: PDB-6xez
  • Surface level: 0.3
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22160.png

Downloads & links

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Map

FileDownload / File: emd_22160.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.3423268 - 2.3366559
Average (Standard dev.)0.0024131667 (±0.05811289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.3422.3370.002

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Supplemental data

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Additional map: map filtered by local resolution

Fileemd_22160_additional.map
Annotationmap filtered by local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 replication/transcription complex bound to nsp13 helic...

EntireName: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
Components
  • Complex: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
    • Protein or peptide: RNA-directed RNA polymerase
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
    • Protein or peptide: Helicase
    • RNA: Product RNA
    • RNA: Template RNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CHAPSO
  • Ligand: ALUMINUM FLUORIDE

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Supramolecule #1: SARS-CoV-2 replication/transcription complex bound to nsp13 helic...

SupramoleculeName: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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: 106.780977 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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: 22.034242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 #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: 9.748385 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPVDMSKMSD VKCTSVVLLS VLQQLRVESS SKLWAQCVQL HNDILLAKDT TEAFEKMVSL LSVLLSMQGA VDINKLCEEM LDNRATLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: Helicase

MacromoleculeName: Helicase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 67.354039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPHMAVGACV LCNSQTSLRC GACIRRPFLC CKCCYDHVIS TSHKLVLSVN PYVCNAPGCD VTDVTQLYLG GMSYYCKSHK PPISFPLCA NGQVFGLYKN TCVGSDNVTD FNAIATCDWT NAGDYILANT CTERLKLFAA ETLKATEETF KLSYGIATVR E VLSDRELH ...String:
GPHMAVGACV LCNSQTSLRC GACIRRPFLC CKCCYDHVIS TSHKLVLSVN PYVCNAPGCD VTDVTQLYLG GMSYYCKSHK PPISFPLCA NGQVFGLYKN TCVGSDNVTD FNAIATCDWT NAGDYILANT CTERLKLFAA ETLKATEETF KLSYGIATVR E VLSDRELH LSWEVGKPRP PLNRNYVFTG YRVTKNSKVQ IGEYTFEKGD YGDAVVYRGT TTYKLNVGDY FVLTSHTVMP LS APTLVPQ EHYVRITGLY PTLNISDEFS SNVANYQKVG MQKYSTLQGP PGTGKSHFAI GLALYYPSAR IVYTACSHAA VDA LCEKAL KYLPIDKCSR IIPARARVEC FDKFKVNSTL EQYVFCTVNA LPETTADIVV FDEISMATNY DLSVVNARLR AKHY VYIGD PAQLPAPRTL LTKGTLEPEY FNSVCRLMKT IGPDMFLGTC RRCPAEIVDT VSALVYDNKL KAHKDKSAQC FKMFY KGVI THDVSSAINR PQIGVVREFL TRNPAWRKAV FISPYNSQNA VASKILGLPT QTVDSSQGSE YDYVIFTQTT ETAHSC NVN RFNVAITRAK VGILCIMSDR DLYDKLQFTS LEIPRRNVAT LQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #5: Product RNA

MacromoleculeName: Product RNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 11.141644 KDa
SequenceString:
CGCGUAGCAU GCUACGUCAU UCUCCUAAGA AGCUA

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Macromolecule #6: Template RNA

MacromoleculeName: Template RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 17.573391 KDa
SequenceString:
CUAUCCCCAU GUGAUUUUAA UAGCUUCUUA GGAGAAUGAC GUAGCAUGCU ACGCG

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #10: CHAPSO

MacromoleculeName: CHAPSO / type: ligand / ID: 10 / Number of copies: 3 / Formula: 1N7
Molecular weightTheoretical: 631.884 Da
Chemical component information

ChemComp-1N7:
CHAPSO / detergent*YM

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Macromolecule #11: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 11 / Number of copies: 2 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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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: 8
GridDetails: unspecified
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: 65.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58942
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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