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- EMDB-23109: SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate -

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Basic information

Entry
Database: EMDB / ID: EMD-23109
TitleSARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate
Map dataSARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate
Sample
  • Complex: SARS-CoV-2 RdRp complex with template:primer and four RMP
    • Complex: RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7
      • 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*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F86)*(F86))-3')
      • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')
KeywordsVIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / 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 / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / 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 / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / 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 / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / 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: 3.89 Å
AuthorsBravo JPK / Taylor DW
Funding support United States, 2 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138348 United States
CitationJournal: Mol Cell / Year: 2021
Title: Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication.
Authors: Jack P K Bravo / Tyler L Dangerfield / David W Taylor / Kenneth A Johnson /
Abstract: Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase ...Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.
History
DepositionDec 14, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l1f
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23109.png

Downloads & links

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Map

FileDownload / File: emd_23109.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 129 pix.
= 141.9 Å		1.1 Å/pix.
x 89 pix.
= 97.9 Å		1.1 Å/pix.
x 85 pix.
= 93.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0511 / Movie #1: 0.1
Minimum - Maximum-0.0017118508 - 1.8140355
Average (Standard dev.)0.021130763 (±0.1027024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin11311993
Dimensions8985129
Spacing8589129
CellA: 93.5 Å / B: 97.9 Å / C: 141.90001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z8589129
origin x/y/z0.0000.0000.000
length x/y/z93.50097.900141.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS11911393
NC/NR/NS8589129
D min/max/mean-0.0021.8140.021

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 RdRp complex with template:primer and four RMP

EntireName: SARS-CoV-2 RdRp complex with template:primer and four RMP
Components
  • Complex: SARS-CoV-2 RdRp complex with template:primer and four RMP
    • Complex: RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7
      • 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*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F86)*(F86))-3')
      • RNA: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')

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Supramolecule #1: SARS-CoV-2 RdRp complex with template:primer and four RMP

SupramoleculeName: SARS-CoV-2 RdRp complex with template:primer and four RMP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: RNA-directed RNA polymerase, Non-structural protein 8, Non-struct...

SupramoleculeName: RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7
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: 103.372164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YRAFDIYNDK VAGFAKFLKT NCCRFQEKDE DDNLIDSYFV VKRHTFSNYQ HEETIYNLLK DCPAVAKHDF FKFRIDGDMV PHISRQRLT KYTMADLVYA LRHFDEGNCD TLKEILVTYN CCDDDYFNKK DWYDFVENPD ILRVYANLGE RVRQALLKTV Q FCDAMRNA ...String:
YRAFDIYNDK VAGFAKFLKT NCCRFQEKDE DDNLIDSYFV VKRHTFSNYQ HEETIYNLLK DCPAVAKHDF FKFRIDGDMV PHISRQRLT KYTMADLVYA LRHFDEGNCD TLKEILVTYN CCDDDYFNKK DWYDFVENPD ILRVYANLGE RVRQALLKTV Q FCDAMRNA GIVGVLTLDN QDLNGNWYDF GDFIQTTPGS GVPVVDSYYS LLMPILTLTR ALTAESHVDT DLTKPYIKWD LL KYDFTEE RLKLFDRYFK YWDQTYHPNC VNCLDDRCIL HCANFNVLFS TVFPPTSFGP LVRKIFVDGV PFVVSTGYHF REL GVVHNQ DVNLHSSRLS FKELLVYAAD PAMHAASGNL LLDKRTTCFS VAALTNNVAF QTVKPGNFNK DFYDFAVSKG FFKE GSSVE LKHFFFAQDG NAAISDYDYY RYNLPTMCDI RQLLFVVEVV DKYFDCYDGG CINANQVIVN NLDKSAGFPF NKWGK ARLY YDSMSYEDQD ALFAYTKRNV IPTITQMNLK YAISAKNRAR TVAGVSICST MTNRQFHQKL LKSIAATRGA TVVIGT SKF YGGWHNMLKT VYSDVENPHL MGWDYPKCDR AMPNMLRIMA SLVLARKHTT CCSLSHRFYR LANECAQVLS EMVMCGG SL YVKPGGTSSG DATTAYANSV FNICQAVTAN VNALLSTDGN KIADKYVRNL QHRLYECLYR NRDVDTDFVN EFYAYLRK H FSMMILSDDA VVCFNSTYAS QGLVASIKNF KSVLYYQNNV FMSEAKCWTE TDLTKGPHEF CSQHTMLVKQ GDDYVYLPY PDPSRILGAG CFVDDIVKTD GTLMIERFVS LAIDAYPLTK HPNQEYADVF HLYLQYIRKL HDELTGHMLD MYSVMLTNDN TSRYWEPEF YEAMYTPHT

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 12.644559 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DKRAKVTSAM QTMLFTMLRK LDNDALNNII NNARDGCVPL NIIPLTTAAK LMVVIPDYNT YKNTCDGTTF TYASALWEIQ QVVDADSKI VQLSEISMDN SPNLAWPLIV TALRA

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: 7.001255 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KMSDVKCTSV VLLSVLQQLR VESSSKLWAQ CVQLHNDILL AKDTTEAFEK MVSLLSVLLS MQG

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F8...

MacromoleculeName: RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F86)*(F86))-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 5.539421 KDa
SequenceString:
CUAAGAAGCU AUU(F86)(F86)(F86)(F86)

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Macromolecule #5: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')

MacromoleculeName: RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 5.657339 KDa
SequenceString:
AUUUUAAUAG CUUCUUAG

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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
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: 80.0 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: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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