+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13116 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Keywords | SARS-CoV-2 / Polymerase / Transcription / Replication / RNA / Dimer / 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent 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 | ||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||||||||||||||||||||
Authors | Jochheim FA / Tegunov D | ||||||||||||||||||||||||
Funding support | Germany, 7 items
| ||||||||||||||||||||||||
Citation | Journal: Commun Biol / Year: 2021 Title: The structure of a dimeric form of SARS-CoV-2 polymerase. Authors: Florian A Jochheim / Dimitry Tegunov / Hauke S Hillen / Jana Schmitzová / Goran Kokic / Christian Dienemann / Patrick Cramer / Abstract: The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic ...The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic subunit nsp12, two copies of subunit nsp8, and one copy of subunit nsp7. Here we report an alternative, dimeric form of the enzyme and resolve its structure at 5.5 Å resolution. In this structure, the two RdRps contain only one copy of nsp8 each and dimerize via their nsp7 subunits to adopt an antiparallel arrangement. We speculate that the RdRp dimer facilitates template switching during production of sub-genomic RNAs. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13116.map.gz | 29.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13116-v30.xml emd-13116.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13116_fsc.xml | 8.7 KB | Display | FSC data file |
Images | emd_13116.png | 53 KB | ||
Masks | emd_13116_msk_1.map | 59.6 MB | Mask map | |
Filedesc metadata | emd-13116.cif.gz | 6.8 KB | ||
Others | emd_13116_half_map_1.map.gz emd_13116_half_map_2.map.gz | 55.2 MB 55.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13116 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13116 | HTTPS FTP |
-Validation report
Summary document | emd_13116_validation.pdf.gz | 903 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_13116_full_validation.pdf.gz | 902.5 KB | Display | |
Data in XML | emd_13116_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_13116_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13116 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13116 | HTTPS FTP |
-Related structure data
Related structure data | 7oygMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10741 (Title: Single particle cryo-EM dataset of Sars-CoV2 Rna dependent RNA polymerase Data size: 2.7 TB Data #1: Unaligned TIF movies of SARS-CoV2 RdRp in complex with nsp7, nsp8 and RNA [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_13116.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.20096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_13116_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map B
File | emd_13116_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map A
File | emd_13116_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase complex (...
Entire | Name: Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) |
---|---|
Components |
|
-Supramolecule #1: Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase complex (...
Supramolecule | Name: Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: SARS-CoV-2 RNA-dependent RNA polymerase (nsp12)
Macromolecule | Name: SARS-CoV-2 RNA-dependent RNA polymerase (nsp12) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 107.053227 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: SARS-CoV-2 nsp8
Macromolecule | Name: SARS-CoV-2 nsp8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.175309 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #3: SARS-CoV-2 nsp7
Macromolecule | Name: SARS-CoV-2 nsp7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 9.521062 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SNASKMSDVK CTSVVLLSVL QQLRVESSSK LWAQCVQLHN DILLAKDTTE AFEKMVSLLS VLLSMQGAVD INKLCEEMLD NRATLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #4: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')
Macromolecule | Name: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3') / type: rna / ID: 4 / Number of copies: 2 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 4.807914 KDa |
Sequence | String: UGAGCCUACG CAGUG |
-Macromolecule #5: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')
Macromolecule | Name: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3') / type: rna / ID: 5 / Number of copies: 2 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 18.138658 KDa |
Sequence | String: UUUUCAUGCA CUGCGUAGGC UCAUACCGUA UUGAGACCUU UUGGUCUCAA UACGGUA |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | 30 deg tilt |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.0014 µm / Calibrated defocus min: 0.0004 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |