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- EMDB-11007: Structure of replicating SARS-CoV-2 polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-11007
TitleStructure of replicating SARS-CoV-2 polymerase
Map dataMain composite map used in refinement.
Sample
  • Complex: RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, nsp7 and duplex RNA.
    • Complex: nsp12
      • Protein or peptide: nsp12
    • Complex: duplex RNA
      • RNA: RNA product
    • Complex: nsp8, nsp7
      • Protein or peptide: nsp8
      • Protein or peptide: nsp7
  • Ligand: ZINC ION
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / transcription, RNA-templated / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / suppression by virus of host toll-like receptor signaling pathway / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive regulation of viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / DNA helicase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / suppression by virus of host type I interferon-mediated signaling pathway / host cell cytoplasm / protein dimerization activity / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus proofreading exoribonuclease / Non-structural protein NSP16, coronavirus-like / Coronavirus RNA-dependent RNA polymerase, N-terminal / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Non-structural protein 14, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 15, middle domain, coronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus endopeptidase C30 / Coronavirus main protease (M-pro) domain profile. / Non-structural protein NSP7 superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein NSP8, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP6 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus papain-like peptidase / RNA synthesis protein NSP10, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHillen HS / Kokic G / Farnung L / Dienemann C / Tegunov D / Cramer P
Funding support Germany, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
European Research Council (ERC)TRANSREGULON Germany
German Research Foundation (DFG)SPP2191 Germany
Volkswagen Foundation Germany
CitationJournal: Nature / Year: 2020
Title: Structure of replicating SARS-CoV-2 polymerase.
Authors: Hauke S Hillen / Goran Kokic / Lucas Farnung / Christian Dienemann / Dimitry Tegunov / Patrick Cramer /
Abstract: The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. ...The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present a cryo-electron microscopy structure of the SARS-CoV-2 RdRp in an active form that mimics the replicating enzyme. The structure comprises the viral proteins non-structural protein 12 (nsp12), nsp8 and nsp7, and more than two turns of RNA template-product duplex. The active-site cleft of nsp12 binds to the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged 'sliding poles'. These sliding poles can account for the known processivity of RdRp that is required for replicating the long genome of coronaviruses. Our results enable a detailed analysis of the inhibitory mechanisms that underlie the antiviral activity of substances such as remdesivir, a drug for the treatment of coronavirus disease 2019 (COVID-19).
History
DepositionMay 6, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yyt
  • Surface level: 3
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11007.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain composite map used in refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 240 pix.
= 200.16 Å
0.83 Å/pix.
x 240 pix.
= 200.16 Å
0.83 Å/pix.
x 240 pix.
= 200.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-15.586838 - 28.571186
Average (Standard dev.)0.016349854 (±0.9739434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 200.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8340.8340.834
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z200.160200.160200.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-15.58728.5710.016

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Supplemental data

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Mask #1

Fileemd_11007_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Mask #2

Fileemd_11007_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Map2 nsp8b focus half map 2.

Fileemd_11007_additional_1.map
AnnotationMap2_nsp8b focus half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Map2 nsp8b focus half map 1.

Fileemd_11007_additional_2.map
AnnotationMap2_nsp8b focus half map 1.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Additional map: Map2 nsp8b class half map 1.

Fileemd_11007_additional_3.map
AnnotationMap2_nsp8b _class half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Map1 core half map 2.

Fileemd_11007_half_map_1.map
AnnotationMap1_core half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Map1 core half map 1.

Fileemd_11007_half_map_2.map
AnnotationMap1_core half map 1.
Projections & Slices
AxesZYX

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Sample components

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Entire : RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, n...

EntireName: RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, nsp7 and duplex RNA.
Components
  • Complex: RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, nsp7 and duplex RNA.
    • Complex: nsp12
      • Protein or peptide: nsp12
    • Complex: duplex RNA
      • RNA: RNA product
    • Complex: nsp8, nsp7
      • Protein or peptide: nsp8
      • Protein or peptide: nsp7
  • Ligand: ZINC ION

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Supramolecule #1: RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, n...

SupramoleculeName: RNA-dependent RNA polymerase complex consisting of nsp12, nsp8, nsp7 and duplex RNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 186 KDa

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Supramolecule #2: nsp12

SupramoleculeName: nsp12 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)

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Supramolecule #3: duplex RNA

SupramoleculeName: duplex RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #4: nsp8, nsp7

SupramoleculeName: nsp8, nsp7 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: nsp12

MacromoleculeName: nsp12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 107.053227 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: SNASADAQSF LNRVCGVSAA RLTPCGTGTS TDVVYRAFDI YNDKVAGFAK FLKTNCCRFQ EKDEDDNLID SYFVVKRHTF SNYQHEETI YNLLKDCPAV AKHDFFKFRI DGDMVPHISR QRLTKYTMAD LVYALRHFDE GNCDTLKEIL VTYNCCDDDY F NKKDWYDF ...String:
SNASADAQSF LNRVCGVSAA RLTPCGTGTS TDVVYRAFDI YNDKVAGFAK FLKTNCCRFQ EKDEDDNLID SYFVVKRHTF SNYQHEETI YNLLKDCPAV AKHDFFKFRI DGDMVPHISR QRLTKYTMAD LVYALRHFDE GNCDTLKEIL VTYNCCDDDY F NKKDWYDF VENPDILRVY ANLGERVRQA LLKTVQFCDA MRNAGIVGVL TLDNQDLNGN WYDFGDFIQT TPGSGVPVVD SY YSLLMPI LTLTRALTAE SHVDTDLTKP YIKWDLLKYD FTEERLKLFD RYFKYWDQTY HPNCVNCLDD RCILHCANFN VLF STVFPP TSFGPLVRKI FVDGVPFVVS TGYHFRELGV VHNQDVNLHS SRLSFKELLV YAADPAMHAA SGNLLLDKRT TCFS VAALT NNVAFQTVKP GNFNKDFYDF AVSKGFFKEG SSVELKHFFF AQDGNAAISD YDYYRYNLPT MCDIRQLLFV VEVVD KYFD CYDGGCINAN QVIVNNLDKS AGFPFNKWGK ARLYYDSMSY EDQDALFAYT KRNVIPTITQ MNLKYAISAK NRARTV AGV SICSTMTNRQ FHQKLLKSIA ATRGATVVIG TSKFYGGWHN MLKTVYSDVE NPHLMGWDYP KCDRAMPNML RIMASLV LA RKHTTCCSLS HRFYRLANEC AQVLSEMVMC GGSLYVKPGG TSSGDATTAY ANSVFNICQA VTANVNALLS TDGNKIAD K YVRNLQHRLY ECLYRNRDVD TDFVNEFYAY LRKHFSMMIL SDDAVVCFNS TYASQGLVAS IKNFKSVLYY QNNVFMSEA KCWTETDLTK GPHEFCSQHT MLVKQGDDYV YLPYPDPSRI LGAGCFVDDI VKTDGTLMIE RFVSLAIDAY PLTKHPNQEY ADVFHLYLQ YIRKLHDELT GHMLDMYSVM LTNDNTSRYW EPEFYEAMYT PHTVLQ

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Macromolecule #2: nsp8

MacromoleculeName: nsp8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.175309 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SNAAIASEFS SLPSYAAFAT AQEAYEQAVA NGDSEVVLKK LKKSLNVAKS EFDRDAAMQR KLEKMADQAM TQMYKQARSE DKRAKVTSA MQTMLFTMLR KLDNDALNNI INNARDGCVP LNIIPLTTAA KLMVVIPDYN TYKNTCDGTT FTYASALWEI Q QVVDADSK ...String:
SNAAIASEFS SLPSYAAFAT AQEAYEQAVA NGDSEVVLKK LKKSLNVAKS EFDRDAAMQR KLEKMADQAM TQMYKQARSE DKRAKVTSA MQTMLFTMLR KLDNDALNNI INNARDGCVP LNIIPLTTAA KLMVVIPDYN TYKNTCDGTT FTYASALWEI Q QVVDADSK IVQLSEISMD NSPNLAWPLI VTALRANSAV KLQ

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Macromolecule #3: nsp7

MacromoleculeName: nsp7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 9.521062 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SNASKMSDVK CTSVVLLSVL QQLRVESSSK LWAQCVQLHN DILLAKDTTE AFEKMVSLLS VLLSMQGAVD INKLCEEMLD NRATLQ

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Macromolecule #4: RNA product

MacromoleculeName: RNA product / type: rna / ID: 4 / Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.687372 KDa
SequenceString:
UUUUCAUGCU ACGCGUAG

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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

BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHepes-NaOH
100.0 mMsodium chlorideNaClSodium chloride
1.0 mMmagnesium chlorideMgCl2
1.0 mMTCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa / Details: 15 mA, Pelco EasyGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8168 / Average exposure time: 2.2 sec. / Average electron dose: 60.0 e/Å2
Details: Images were collected at 30 degree stage tilt. Non-superres.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1300000
CTF correctionSoftware - Name: Warp (ver. 1.07 BETA)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 418000

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A / Chain - Residue range: 1-930
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6yyt:
Structure of replicating SARS-CoV-2 polymerase

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