[English] 日本語
Yorodumi
- EMDB-34318: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34318
TitleA mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Map data
Sample
  • Complex: E-RTC_UMP-nsp9_GMPPNP
    • Complex: Replicase polyprotein
      • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase
      • Protein or peptide: Non-structural protein 8
      • Protein or peptide: Non-structural protein 7
      • Protein or peptide: Helicase
      • Protein or peptide: Non-structural protein 9
    • Complex: RNA
      • RNA: RNA (25-MER)
      • RNA: template
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Function / homology
Function and homology information


viral genome replication / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / endopeptidase complex ...viral genome replication / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / 5'-3' RNA helicase activity / mRNA cap binding complex / Transcription of SARS-CoV-2 sgRNAs / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / Translation of Replicase and Assembly of the Replication Transcription Complex / mRNA methylation / Replication of the SARS-CoV-2 genome / modulation by virus of host autophagy / double membrane vesicle viral factory outer membrane / snRNP Assembly / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / TRAF3-dependent IRF activation pathway / suppression by virus of host type I interferon production / host cell endosome / mRNA guanylyltransferase / cytoplasmic viral factory / induction by virus of catabolism of host mRNA / SARS-CoV-2 modulates host translation machinery / protein K48-linked deubiquitination / 3'-5'-RNA exonuclease activity / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / RNA-templated transcription / 7-methylguanosine mRNA capping / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral transcription / suppression by virus of host NF-kappaB cascade / suppression by virus of host toll-like receptor signaling pathway / modulation by symbiont of host protein ubiquitination / mRNA (guanine-N7)-methyltransferase / protein K63-linked deubiquitination / host cell endoplasmic reticulum / methyltransferase cap1 / host cell Golgi apparatus / positive stranded viral RNA replication / suppression by virus of host TRAF-mediated signal transduction / positive regulation of viral genome replication / protein autoprocessing / mRNA (nucleoside-2'-O-)-methyltransferase activity / cysteine-type peptidase activity / mRNA (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / DNA helicase / helicase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / transferase activity / protein processing / host cell perinuclear region of cytoplasm / endonuclease activity / viral protein processing / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / copper ion binding / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / host cell cytoplasm / protein dimerization activity / DNA-templated transcription / lipid binding / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / protein homodimerization activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 14, betacoronavirus / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 14, betacoronavirus / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2-O-methyltransferase / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / 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 / Viral (Superfamily 1) RNA helicase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / 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 / Coronavirus 2'-O-methyltransferase / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / 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 / (+) 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 / NSP1 globular domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Lipocalin signature. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Coronavirus Nsp3 Y3 domain profile. / Betacoronavirus Nsp3c-M domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / 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. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYan LM / Huang YC / Ge J / Liu ZY / Gao Y / Rao ZH / Lou ZY
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0707500 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
CitationJournal: Cell / Year: 2022
Title: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
Authors: Liming Yan / Yucen Huang / Ji Ge / Zhenyu Liu / Pengchi Lu / Bo Huang / Shan Gao / Junbo Wang / Liping Tan / Sihan Ye / Fengxi Yu / Weiqi Lan / Shiya Xu / Feng Zhou / Lei Shi / Luke W Guddat ...Authors: Liming Yan / Yucen Huang / Ji Ge / Zhenyu Liu / Pengchi Lu / Bo Huang / Shan Gao / Junbo Wang / Liping Tan / Sihan Ye / Fengxi Yu / Weiqi Lan / Shiya Xu / Feng Zhou / Lei Shi / Luke W Guddat / Yan Gao / Zihe Rao / Zhiyong Lou /
Abstract: Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The ...Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.
History
DepositionSep 17, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_34318.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å
0.82 Å/pix.
x 512 pix.
= 419.84 Å
0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9911224 - 1.816654
Average (Standard dev.)-9.8002856e-05 (±0.03804575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_34318_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_34318_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : E-RTC_UMP-nsp9_GMPPNP

EntireName: E-RTC_UMP-nsp9_GMPPNP
Components
  • Complex: E-RTC_UMP-nsp9_GMPPNP
    • Complex: Replicase polyprotein
      • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase
      • Protein or peptide: Non-structural protein 8
      • Protein or peptide: Non-structural protein 7
      • Protein or peptide: Helicase
      • Protein or peptide: Non-structural protein 9
    • Complex: RNA
      • RNA: RNA (25-MER)
      • RNA: template
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

+
Supramolecule #1: E-RTC_UMP-nsp9_GMPPNP

SupramoleculeName: E-RTC_UMP-nsp9_GMPPNP / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

+
Supramolecule #2: Replicase polyprotein

SupramoleculeName: Replicase polyprotein / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #6-#7

+
Supramolecule #3: RNA

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

+
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: 106.780977 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN ...String:
SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN PDILRVYANL GERVRQALLK TVQFCDAMRN AGIVGVLTLD NQDLNGNWYD FGDFIQTTPG SGVPVVDSYY SL LMPILTL TRALTAESHV DTDLTKPYIK WDLLKYDFTE ERLKLFDRYF KYWDQTYHPN CVNCLDDRCI LHCANFNVLF STV FPPTSF GPLVRKIFVD GVPFVVSTGY HFRELGVVHN QDVNLHSSRL SFKELLVYAA DPAMHAASGN LLLDKRTTCF SVAA LTNNV AFQTVKPGNF NKDFYDFAVS KGFFKEGSSV ELKHFFFAQD GNAAISDYDY YRYNLPTMCD IRQLLFVVEV VDKYF DCYD GGCINANQVI VNNLDKSAGF PFNKWGKARL YYDSMSYEDQ DALFAYTKRN VIPTITQMNL KYAISAKNRA RTVAGV SIC STMTNRQFHQ KLLKSIAATR GATVVIGTSK FYGGWHNMLK TVYSDVENPH LMGWDYPKCD RAMPNMLRIM ASLVLAR KH TTCCSLSHRF YRLANECAQV LSEMVMCGGS LYVKPGGTSS GDATTAYANS VFNICQAVTA NVNALLSTDG NKIADKYV R NLQHRLYECL YRNRDVDTDF VNEFYAYLRK HFSMMILSDD AVVCFNSTYA SQGLVASIKN FKSVLYYQNN VFMSEAKCW TETDLTKGPH EFCSQHTMLV KQGDDYVYLP YPDPSRILGA GCFVDDIVKT DGTLMIERFV SLAIDAYPLT KHPNQEYADV FHLYLQYIR KLHDELTGHM LDMYSVMLTN DNTSRYWEPE FYEAMYTPHT VLQ

+
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: 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

+
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: 9.248804 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SKMSDVKCTS VVLLSVLQQL RVESSSKLWA QCVQLHNDIL LAKDTTEAFE KMVSLLSVLL SMQGAVDINK LCEEMLDNRA TLQ

+
Macromolecule #6: Helicase

MacromoleculeName: Helicase / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 66.930531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AVGACVLCNS QTSLRCGACI RRPFLCCKCC YDHVISTSHK LVLSVNPYVC NAPGCDVTDV TQLYLGGMSY YCKSHKPPIS FPLCANGQV FGLYKNTCVG SDNVTDFNAI ATCDWTNAGD YILANTCTER LKLFAAETLK ATEETFKLSY GIATVREVLS D RELHLSWE ...String:
AVGACVLCNS QTSLRCGACI RRPFLCCKCC YDHVISTSHK LVLSVNPYVC NAPGCDVTDV TQLYLGGMSY YCKSHKPPIS FPLCANGQV FGLYKNTCVG SDNVTDFNAI ATCDWTNAGD YILANTCTER LKLFAAETLK ATEETFKLSY GIATVREVLS D RELHLSWE VGKPRPPLNR NYVFTGYRVT KNSKVQIGEY TFEKGDYGDA VVYRGTTTYK LNVGDYFVLT SHTVMPLSAP TL VPQEHYV RITGLYPTLN ISDEFSSNVA NYQKVGMQKY STLQGPPGTG KSHFAIGLAL YYPSARIVYT ACSHAAVDAL CEK ALKYLP IDKCSRIIPA RARVECFDKF KVNSTLEQYV FCTVNALPET TADIVVFDEI SMATNYDLSV VNARLRAKHY VYIG DPAQL PAPRTLLTKG TLEPEYFNSV CRLMKTIGPD MFLGTCRRCP AEIVDTVSAL VYDNKLKAHK DKSAQCFKMF YKGVI THDV SSAINRPQIG VVREFLTRNP AWRKAVFISP YNSQNAVASK ILGLPTQTVD SSQGSEYDYV IFTQTTETAH SCNVNR FNV AITRAKVGIL CIMSDRDLYD KLQFTSLEIP RRNVATLQ

+
Macromolecule #7: Non-structural protein 9

MacromoleculeName: Non-structural protein 9 / type: protein_or_peptide / ID: 7
Details: Uridine monophosphate bound to to N-terminal of chain G
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 12.697337 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
UNNELSPVAL RQMSCAAGTT QTACTDDNAL AYYNTTKGGR FVLALLSDLQ DLKWARFPKS DGTGTIYTEL EPPCRFVTDT PKGPKVKYL YFIKGLNNLN RGMVLGSLAA TVRLQ

+
Macromolecule #4: RNA (25-MER)

MacromoleculeName: RNA (25-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.172932 KDa
SequenceString:
GCGGUAGUAG CAUGCUAGGG AGCAG

+
Macromolecule #5: template

MacromoleculeName: template / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.443209 KDa
SequenceString:
AAUGUCUGAC UGCUCCCUAG CAUGCUACUA CCG

+
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #9: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2058771

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more