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- EMDB-31061: A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase -

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Entry
Database: EMDB / ID: EMD-31061
TitleA dual mechanism of action of AT-527 against SARS-CoV-2 polymerase
Map data
Sample
  • Complex: nsp12-nsp7-nsp8-RNA-AT9010
    • Complex: nsp12-nsp7-nsp8
      • Protein or peptide: RNA-directed RNA polymerase
      • Protein or peptide: Non-structural protein 8
      • Protein or peptide: Non-structural protein 7
    • Complex: RNA
      • 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*(AT9))-3')
      • RNA: RNA (5'-R(P*CP*CP*CP*CP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
KeywordsSARS-CoV-2 / nsp12 / NiRAN / RdRp / AT-9010 / AT-527 / VIRAL PROTEIN
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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / 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 / lipid binding / DNA-templated transcription / 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 / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsShannon A / Fattorini V
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase.
Authors: Ashleigh Shannon / Véronique Fattorini / Bhawna Sama / Barbara Selisko / Mikael Feracci / Camille Falcou / Pierre Gauffre / Priscila El Kazzi / Adrien Delpal / Etienne Decroly / Karine ...Authors: Ashleigh Shannon / Véronique Fattorini / Bhawna Sama / Barbara Selisko / Mikael Feracci / Camille Falcou / Pierre Gauffre / Priscila El Kazzi / Adrien Delpal / Etienne Decroly / Karine Alvarez / Cécilia Eydoux / Jean-Claude Guillemot / Adel Moussa / Steven S Good / Paolo La Colla / Kai Lin / Jean-Pierre Sommadossi / Yingxiao Zhu / Xiaodong Yan / Hui Shi / François Ferron / Bruno Canard /
Abstract: The guanosine analog AT-527 represents a promising candidate against Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2). AT-527 recently entered phase III clinical trials for the ...The guanosine analog AT-527 represents a promising candidate against Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2). AT-527 recently entered phase III clinical trials for the treatment of COVID-19. Once in cells, AT-527 is converted into its triphosphate form, AT-9010, that presumably targets the viral RNA-dependent RNA polymerase (RdRp, nsp12), for incorporation into viral RNA. Here we report a 2.98 Å cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-nsp8-RNA complex, showing AT-9010 bound at three sites of nsp12. In the RdRp active-site, one AT-9010 is incorporated at the 3' end of the RNA product strand. Its modified ribose group (2'-fluoro, 2'-methyl) prevents correct alignment of the incoming NTP, in this case a second AT-9010, causing immediate termination of RNA synthesis. The third AT-9010 is bound to the N-terminal domain of nsp12 - known as the NiRAN. In contrast to native NTPs, AT-9010 is in a flipped orientation in the active-site, with its guanine base unexpectedly occupying a previously unnoticed cavity. AT-9010 outcompetes all native nucleotides for NiRAN binding, inhibiting its nucleotidyltransferase activity. The dual mechanism of action of AT-527 at both RdRp and NiRAN active sites represents a promising research avenue against COVID-19.
History
DepositionMar 15, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.214
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.214
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  • Surface view with fitted model
  • Atomic models: PDB-7ed5
  • Surface level: 0.214
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31061.png

Downloads & links

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Map

FileDownload / File: emd_31061.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.214 / Movie #1: 0.214
Minimum - Maximum-0.49555314 - 1.0168804
Average (Standard dev.)0.0010246771 (±0.027704764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z265.600265.600265.600
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.4961.0170.001

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Supplemental data

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Mask #1

Fileemd_31061_msk_1.map
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Half map: #1

Fileemd_31061_half_map_1.map
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Half map: #2

Fileemd_31061_half_map_2.map
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Sample components

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Entire : nsp12-nsp7-nsp8-RNA-AT9010

EntireName: nsp12-nsp7-nsp8-RNA-AT9010
Components
  • Complex: nsp12-nsp7-nsp8-RNA-AT9010
    • Complex: nsp12-nsp7-nsp8
      • Protein or peptide: RNA-directed RNA polymerase
      • Protein or peptide: Non-structural protein 8
      • Protein or peptide: Non-structural protein 7
    • Complex: RNA
      • 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*(AT9))-3')
      • RNA: RNA (5'-R(P*CP*CP*CP*CP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

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Supramolecule #1: nsp12-nsp7-nsp8-RNA-AT9010

SupramoleculeName: nsp12-nsp7-nsp8-RNA-AT9010 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 160 KDa

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Supramolecule #2: nsp12-nsp7-nsp8

SupramoleculeName: nsp12-nsp7-nsp8 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5

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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: 109.911383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHW SHPQFEKENL YFQGSADAQS FLNRVCGVSA ARLTPCGTGT STDVVYRAFD IYNDKVAGFA KFLKTNCCRF QEKDEDDNL IDSYFVVKRH TFSNYQHEET IYNLLKDCPA VAKHDFFKFR IDGDMVPHIS RQRLTKYTMA DLVYALRHFD E GNCDTLKE ...String:
MHHHHHHHHW SHPQFEKENL YFQGSADAQS FLNRVCGVSA ARLTPCGTGT STDVVYRAFD IYNDKVAGFA KFLKTNCCRF QEKDEDDNL IDSYFVVKRH TFSNYQHEET IYNLLKDCPA VAKHDFFKFR IDGDMVPHIS RQRLTKYTMA DLVYALRHFD E GNCDTLKE ILVTYNCCDD DYFNKKDWYD FVENPDILRV YANLGERVRQ ALLKTVQFCD AMRNAGIVGV LTLDNQDLNG NW YDFGDFI QTTPGSGVPV VDSYYSLLMP ILTLTRALTA ESHVDTDLTK PYIKWDLLKY DFTEERLKLF DRYFKYWDQT YHP NCVNCL DDRCILHCAN FNVLFSTVFP PTSFGPLVRK IFVDGVPFVV STGYHFRELG VVHNQDVNLH SSRLSFKELL VYAA DPAMH AASGNLLLDK RTTCFSVAAL TNNVAFQTVK PGNFNKDFYD FAVSKGFFKE GSSVELKHFF FAQDGNAAIS DYDYY RYNL PTMCDIRQLL FVVEVVDKYF DCYDGGCINA NQVIVNNLDK SAGFPFNKWG KARLYYDSMS YEDQDALFAY TKRNVI PTI TQMNLKYAIS AKNRARTVAG VSICSTMTNR QFHQKLLKSI AATRGATVVI GTSKFYGGWH NMLKTVYSDV ENPHLMG WD YPKCDRAMPN MLRIMASLVL ARKHTTCCSL SHRFYRLANE CAQVLSEMVM CGGSLYVKPG GTSSGDATTA YANSVFNI C QAVTANVNAL LSTDGNKIAD KYVRNLQHRL YECLYRNRDV DTDFVNEFYA YLRKHFSMMI LSDDAVVCFN STYASQGLV ASIKNFKSVL YYQNNVFMSE AKCWTETDLT KGPHEFCSQH TMLVKQGDDY VYLPYPDPSR ILGAGCFVDD IVKTDGTLMI ERFVSLAID AYPLTKHPNQ EYADVFHLYL QYIRKLHDEL TGHMLDMYSV MLTNDNTSRY WEPEFYEAMY TPHTVLQ

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: 24.712006 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHDYK DDDDKENLYF QGAIASEFSS LPSYAAFATA QEAYEQAVAN GDSEVVLKKL KKSLNVAKSE FDRDAAMQRK LEKMADQAM TQMYKQARSE DKRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT Y KNTCDGTT ...String:
MHHHHHHDYK DDDDKENLYF QGAIASEFSS LPSYAAFATA QEAYEQAVAN GDSEVVLKKL KKSLNVAKSE FDRDAAMQRK LEKMADQAM TQMYKQARSE DKRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT Y KNTCDGTT FTYASALWEI QQVVDADSKI 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: 12.337141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSKMSDVKCT SVVLLSVLQQ LRVESSSKLW AQCVQLHNDI LLAKDTTEAF EKMVSLLSVL LSMQGAVDIN KLCEEMLDNR ATLQGGGGS GLNDIFEAQK IEWHEHHHHH H

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: 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*(AT9))-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.410816 KDa
SequenceString:
GCUAUGUGAG AUUAAGUUAU

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

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*CP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP*GP*C)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.348616 KDa
SequenceString:
CCCCCCCCCC AUAACUUAAU CUCACAUAGC

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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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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluo...

MacromoleculeName: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
type: ligand / ID: 8 / Number of copies: 3 / Formula: AT9
Molecular weightTheoretical: 539.198 Da
Chemical component information

ChemComp-AT9:
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

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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: 8
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: 1.61 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio generated model in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181669
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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