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- EMDB-11995: Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase w... -

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Basic information

Entry
Database: EMDB / ID: EMD-11995
TitleStructure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)
Map dataDenoised main map.
Sample
  • Complex: SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.
    • Complex: SARS-CoV-2 RNA-dependent RNA polymerase nsp12
      • Protein or peptide: SARS-CoV-2 RNA-dependent RNA polymerase nsp12
    • Complex: SARS-CoV-2 nsp7 and 8
      • Protein or peptide: SARS-CoV-2 nsp8
      • Protein or peptide: SARS-CoV-2 nsp7
    • Complex: DNA and RNA
      • RNA: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')
      • RNA: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')
  • Ligand: ZINC ION
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus
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
AuthorsKokic G / Hillen HS / Tegunov D / Dienemann C / Seitz F / Schmitzova J / Farnung L / Siewert A / Hoebartner C / Cramer P
Funding support Germany, 7 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SPP2191 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP1784 Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
European Research Council (ERC)693023 Germany
European Research Council (ERC)682586 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.
Authors: Goran Kokic / Hauke S Hillen / Dimitry Tegunov / Christian Dienemann / Florian Seitz / Jana Schmitzova / Lucas Farnung / Aaron Siewert / Claudia Höbartner / Patrick Cramer /
Abstract: Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of ...Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3'-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3'-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3'-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.
History
DepositionNov 30, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0003
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  • Surface view with fitted model
  • Atomic models: PDB-7b3d
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11995.png

Downloads & links

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Map

FileDownload / File: emd_11995.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDenoised main map.
Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 0.0003 / Movie #1: 0.0003
Minimum - Maximum-0.00090332614 - 0.0017360445
Average (Standard dev.)2.1078765e-06 (±4.1083505e-05)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0010.0020.000

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Supplemental data

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Mask #1

Fileemd_11995_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_11995_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_11995_half_map_2.map
AnnotationHalf map 1
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 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp...

EntireName: SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.
Components
  • Complex: SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.
    • Complex: SARS-CoV-2 RNA-dependent RNA polymerase nsp12
      • Protein or peptide: SARS-CoV-2 RNA-dependent RNA polymerase nsp12
    • Complex: SARS-CoV-2 nsp7 and 8
      • Protein or peptide: SARS-CoV-2 nsp8
      • Protein or peptide: SARS-CoV-2 nsp7
    • Complex: DNA and RNA
      • RNA: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')
      • RNA: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')
  • Ligand: ZINC ION

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Supramolecule #1: SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp...

SupramoleculeName: SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: SARS-CoV-2 RNA-dependent RNA polymerase nsp12

SupramoleculeName: SARS-CoV-2 RNA-dependent RNA polymerase nsp12 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: SARS-CoV-2 nsp7 and 8

SupramoleculeName: SARS-CoV-2 nsp7 and 8 / type: complex / ID: 3 / 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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Supramolecule #4: DNA and RNA

SupramoleculeName: DNA and RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: SARS-CoV-2 RNA-dependent RNA polymerase nsp12

MacromoleculeName: SARS-CoV-2 RNA-dependent RNA polymerase 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: Trichoplusia ni (cabbage looper)
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: SARS-CoV-2 nsp8

MacromoleculeName: SARS-CoV-2 nsp8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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: SARS-CoV-2 nsp7

MacromoleculeName: SARS-CoV-2 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 (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')

MacromoleculeName: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 4.807914 KDa
SequenceString:
UGAGCCUACG CAGUG

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

MacromoleculeName: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3') / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 18.138658 KDa
SequenceString:
UUUUCAUGCA CUGCGUAGGC UCAUACCGUA UUGAGACCUU UUGGUCUCAA UACGGUA

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
20.0 mMHepes
100.0 mMNaClSodium chloride
1.0 mMMgCl2
1.0 mMTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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 defocus max: 0.0017 µm / Calibrated defocus min: 0.0004 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / 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
Details30 deg tilt.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1767915
CTF correctionSoftware - Name: Warp (ver. 1.0.7)
Startup modelType of model: EMDB MAP
EMDB ID:

11007

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Details: M was used / Number images used: 819273

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Atomic model buiding 1

Initial modelPDB ID:

6yyt

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7b3d:
Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)

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