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- EMDB-54695: Cryo-EM structure of SARS CoV-2 RdRp wild-type in complex with 20... -

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Entry
Database: EMDB / ID: EMD-54695
TitleCryo-EM structure of SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating ATP
Map data
Sample
  • Complex: SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating ATP
    • RNA: RNA primer strand (27-MER)
    • RNA: RNA template strand (40-MER)
    • Protein or peptide: RNA-directed RNA polymerase nsp12
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
  • Ligand: ZINC ION
KeywordsRNA-dependent RNA polymerase / SARS CoV-2 / transcription / viral protein / ATP / remdesivir / S759A mutant
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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell nucleus / 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: 2.8 Å
AuthorsOliva MF / Das K
Funding support Belgium, 1 items
OrganizationGrant numberCountry
KU Leuven Belgium
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance.
Authors: Calvin J Gordon / Mizar F Oliva / Hery W Lee / Quinten Goovaerts / Brent De Wijngaert / Matthias Götte / Kalyan Das
Abstract: Nucleoside analogs (NAs) have been successfully used to treat viral infections. dNTP analogs are primarily DNA chain terminators, while NTP analogs, such as remdesivir, can inhibit as delayed chain ...Nucleoside analogs (NAs) have been successfully used to treat viral infections. dNTP analogs are primarily DNA chain terminators, while NTP analogs, such as remdesivir, can inhibit as delayed chain terminators or when in the template strand. Determining the frequency of remdesivir triphosphate (RTP) incorporation in the presence of the competing ATP can help in understanding different modes of viral RNA-dependent RNA polymerase (RdRp) inhibition by NTP analogs. We employed enzymatic assays, mass spectrometry, and cryo-EM to show that SARS-CoV-2 RdRp preferentially incorporates RTP, outcompeting 10-fold higher ATP concentration; however, successive RTP incorporations are less favoured when ATP is present. Structures of SARS-CoV-2 RdRp in this and previous studies demonstrate resilience of remdesivir:UMP base pair to translocation, explaining the reduced preference for conjugate incorporations. Together, the RTP versus ATP incorporation is driven by their relative concentration and structural rigidity of remdesivir:UMP, ultimately limiting the number of incorporated remdesivir in a fully synthesized RNA strand. The S759A mutant confers RTP resistance, and the structures of S759A RdRp catalytic complexes reveal that altered ribose-ring conformation and repositioning of the primer 3'-end nucleotide contribute to RTP resistance. These findings enhance our understanding of non-obligate NTP analogs and provide insight into S759A resistance mechanism.
History
DepositionAug 7, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54695.png

Downloads & links

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Map

FileDownload / File: emd_54695.map.gz / Format: CCP4 / Size: 15.6 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.)
0.9 Å/pix.
x 160 pix.
= 144. Å		0.9 Å/pix.
x 160 pix.
= 144. Å		0.9 Å/pix.
x 160 pix.
= 144. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0062
Minimum - Maximum-0.04120943 - 0.07019061
Average (Standard dev.)0.000049236274 (±0.0041623395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 144.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54695_msk_1.map
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Half map: #2

Fileemd_54695_half_map_1.map
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Half map: #1

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Sample components

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Entire : SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporat...

EntireName: SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating ATP
Components
  • Complex: SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating ATP
    • RNA: RNA primer strand (27-MER)
    • RNA: RNA template strand (40-MER)
    • Protein or peptide: RNA-directed RNA polymerase nsp12
    • Protein or peptide: Non-structural protein 8
    • Protein or peptide: Non-structural protein 7
  • Ligand: ZINC ION

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Supramolecule #1: SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporat...

SupramoleculeName: SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: RNA primer strand (27-MER)

MacromoleculeName: RNA primer strand (27-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 8.56412 KDa
SequenceString:
GUCAUUCUCC UAAGAAGCUA UUAAAAU

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Macromolecule #2: RNA template strand (40-MER)

MacromoleculeName: RNA template strand (40-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 12.720521 KDa
SequenceString:
CUAUCCCCAU GUGAUUUUAA UAGCUUCUUA GGAGAAUGAC

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Macromolecule #3: RNA-directed RNA polymerase nsp12

MacromoleculeName: RNA-directed RNA polymerase nsp12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 106.436648 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: QSFLNRVCGV SAARLTPCGT GTSTDVVYRA FDIYNDKVAG FAKFLKTNCC RFQEKDEDDN LIDSYFVVKR HTFSNYQHEE TIYNLLKDC PAVAKHDFFK FRIDGDMVPH ISRQRLTKYT MADLVYALRH FDEGNCDTLK EILVTYNCCD DDYFNKKDWY D FVENPDIL ...String:
QSFLNRVCGV SAARLTPCGT GTSTDVVYRA FDIYNDKVAG FAKFLKTNCC RFQEKDEDDN LIDSYFVVKR HTFSNYQHEE TIYNLLKDC PAVAKHDFFK FRIDGDMVPH ISRQRLTKYT MADLVYALRH FDEGNCDTLK EILVTYNCCD DDYFNKKDWY D FVENPDIL RVYANLGERV RQALLKTVQF CDAMRNAGIV GVLTLDNQDL NGNWYDFGDF IQTTPGSGVP VVDSYYSLLM PI LTLTRAL TAESHVDTDL TKPYIKWDLL KYDFTEERLK LFDRYFKYWD QTYHPNCVNC LDDRCILHCA NFNVLFSTVF PPT SFGPLV RKIFVDGVPF VVSTGYHFRE LGVVHNQDVN LHSSRLSFKE LLVYAADPAM HAASGNLLLD KRTTCFSVAA LTNN VAFQT VKPGNFNKDF YDFAVSKGFF KEGSSVELKH FFFAQDGNAA ISDYDYYRYN LPTMCDIRQL LFVVEVVDKY FDCYD GGCI NANQVIVNNL DKSAGFPFNK WGKARLYYDS MSYEDQDALF AYTKRNVIPT ITQMNLKYAI SAKNRARTVA GVSICS TMT NRQFHQKLLK SIAATRGATV VIGTSKFYGG WHNMLKTVYS DVENPHLMGW DYPKCDRAMP NMLRIMASLV LARKHTT CC SLSHRFYRLA NECAQVLSEM VMCGGSLYVK PGGTSSGDAT TAYANSVFNI CQAVTANVNA LLSTDGNKIA DKYVRNLQ H RLYECLYRNR DVDTDFVNEF YAYLRKHFSM MILSDDAVVC FNSTYASQGL VASIKNFKSV LYYQNNVFMS EAKCWTETD LTKGPHEFCS QHTMLVKQGD DYVYLPYPDP SRILGAGCFV DDIVKTDGTL MIERFVSLAI DAYPLTKHPN QEYADVFHLY LQYIRKLHD ELTGHMLDMY SVMLTNDNTS RYWEPEFYEA MYTPHTVLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #4: Non-structural protein 8

MacromoleculeName: Non-structural protein 8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.903047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AIASEFSSLP SYAAFATAQE AYEQAVANGD SEVVLKKLKK SLNVAKSEFD RDAAMQRKLE KMADQAMTQM YKQARSEDKR AKVTSAMQT MLFTMLRKLD NDALNNIINN ARDGCVPLNI IPLTTAAKLM VVIPDYNTYK NTCDGTTFTY ASALWEIQQV V DADSKIVQ ...String:
AIASEFSSLP SYAAFATAQE AYEQAVANGD SEVVLKKLKK SLNVAKSEFD RDAAMQRKLE KMADQAMTQM YKQARSEDKR AKVTSAMQT MLFTMLRKLD NDALNNIINN ARDGCVPLNI IPLTTAAKLM VVIPDYNTYK NTCDGTTFTY ASALWEIQQV V DADSKIVQ LSEISMDNSP NLAWPLIVTA LRANSAVKLQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #5: Non-structural protein 7

MacromoleculeName: Non-structural protein 7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 9.248804 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SKMSDVKCTS VVLLSVLQQL RVESSSKLWA QCVQLHNDIL LAKDTTEAFE KMVSLLSVLL SMQGAVDINK LCEEMLDNRA TLQ

UniProtKB: Replicase polyprotein 1ab

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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

BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 75 mM NaCl, 5 mM MgCl2, 5 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dok

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 109207
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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