+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23971 | |||||||||||||||
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Title | SARS-CoV-2 Nsp2 | |||||||||||||||
Map data | SARS-CoV-2 Nsp2 main map | |||||||||||||||
Sample |
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Keywords | Nsp2 / virus infection / SARS-CoV-2 / Orf1a / 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: 3.15 Å | |||||||||||||||
Authors | QCRG Structural Biology Consortium | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: bioRxiv / Year: 2021 Title: CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Authors: Meghna Gupta / Caleigh M Azumaya / Michelle Moritz / Sergei Pourmal / Amy Diallo / Gregory E Merz / Gwendolyn Jang / Mehdi Bouhaddou / Andrea Fossati / Axel F Brilot / Devan Diwanji / Evelyn ...Authors: Meghna Gupta / Caleigh M Azumaya / Michelle Moritz / Sergei Pourmal / Amy Diallo / Gregory E Merz / Gwendolyn Jang / Mehdi Bouhaddou / Andrea Fossati / Axel F Brilot / Devan Diwanji / Evelyn Hernandez / Nadia Herrera / Huong T Kratochvil / Victor L Lam / Fei Li / Yang Li / Henry C Nguyen / Carlos Nowotny / Tristan W Owens / Jessica K Peters / Alexandrea N Rizo / Ursula Schulze-Gahmen / Amber M Smith / Iris D Young / Zanlin Yu / Daniel Asarnow / Christian Billesbølle / Melody G Campbell / Jen Chen / Kuei-Ho Chen / Un Seng Chio / Miles Sasha Dickinson / Loan Doan / Mingliang Jin / Kate Kim / Junrui Li / Yen-Li Li / Edmond Linossi / Yanxin Liu / Megan Lo / Jocelyne Lopez / Kyle E Lopez / Adamo Mancino / Frank R Moss / Michael D Paul / Komal Ishwar Pawar / Adrian Pelin / Thomas H Pospiech / Cristina Puchades / Soumya Govinda Remesh / Maliheh Safari / Kaitlin Schaefer / Ming Sun / Mariano C Tabios / Aye C Thwin / Erron W Titus / Raphael Trenker / Eric Tse / Tsz Kin Martin Tsui / Feng Wang / Kaihua Zhang / Yang Zhang / Jianhua Zhao / Fengbo Zhou / Yuan Zhou / Lorena Zuliani-Alvarez / / David A Agard / Yifan Cheng / James S Fraser / Natalia Jura / Tanja Kortemme / Aashish Manglik / Daniel R Southworth / Robert M Stroud / Danielle L Swaney / Nevan J Krogan / Adam Frost / Oren S Rosenberg / Kliment A Verba / Abstract: The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic ...The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23971.map.gz | 78.4 MB | EMDB map data format | |
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Header (meta data) | emd-23971-v30.xml emd-23971.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23971_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_23971.png | 55.9 KB | ||
Masks | emd_23971_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-23971.cif.gz | 6 KB | ||
Others | emd_23971_half_map_1.map.gz emd_23971_half_map_2.map.gz | 65.4 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23971 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23971 | HTTPS FTP |
-Validation report
Summary document | emd_23971_validation.pdf.gz | 813.3 KB | Display | EMDB validaton report |
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Full document | emd_23971_full_validation.pdf.gz | 812.9 KB | Display | |
Data in XML | emd_23971_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_23971_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23971 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23971 | HTTPS FTP |
-Related structure data
Related structure data | 7msxMC 7mswC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23971.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 Nsp2 main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23971_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 Nsp2 half map - odd
File | emd_23971_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 Nsp2 half map - odd | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 Nsp2 half map - even
File | emd_23971_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 Nsp2 half map - even | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Nsp2
Entire | Name: SARS-CoV-2 Nsp2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Nsp2
Supramolecule | Name: SARS-CoV-2 Nsp2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 71 KDa |
-Macromolecule #1: Non-structural protein 2
Macromolecule | Name: Non-structural protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 70.590219 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AYTRYVDNNF CGPDGYPLEC IKDLLARAGK ASCTLSEQLD FIDTKRGVYC CREHEHEIAW YTERSEKSYE LQTPFEIKLA KKFDTFNGE CPNFVFPLNS IIKTIQPRVE KKKLDGFMGR IRSVYPVASP NECNQMCLST LMKCDHCGET SWQTGDFVKA T CEFCGTEN ...String: AYTRYVDNNF CGPDGYPLEC IKDLLARAGK ASCTLSEQLD FIDTKRGVYC CREHEHEIAW YTERSEKSYE LQTPFEIKLA KKFDTFNGE CPNFVFPLNS IIKTIQPRVE KKKLDGFMGR IRSVYPVASP NECNQMCLST LMKCDHCGET SWQTGDFVKA T CEFCGTEN LTKEGATTCG YLPQNAVVKI YCPACHNSEV GPEHSLAEYH NESGLKTILR KGGRTIAFGG CVFSYVGCHN KC AYWVPRA SANIGCNHTG VVGEGSEGLN DNLLEILQKE KVNINIVGDF KLNEEIAIIL ASFSASTSAF VETVKGLDYK AFK QIVESC GNFKVTKGKA KKGAWNIGEQ KSILSPLYAF ASEAARVVRS IFSRTLETAQ NSVRVLQKAA ITILDGISQY SLRL IDAMM FTSDLATNNL VVMAYITGGV VQLTSQWLTN IFGTVYEKLK PVLDWLEEKF KEGVEFLRDG WEIVKFISTC ACEIV GGQI VTCAKEIKES VQTFFKLVNK FLALCADSII IGGAKLKALN LGETFVTHSK GLYRKCVKSR EETGLLMPLK APKEII FLE GETLPTEVLT EEVVLKTGDL QPLEQPTSEA VEAPLVGTPV CINGLMLLEI KDTEKYCALA PNMMVTNNTF TLKGG UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.39 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: Filtered and degassed before running FPLC | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 4 seconds before plunging into liquid ethane. | |||||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 1920 / Average electron dose: 66.0 e/Å2 Details: Data was collected in two sessions; 804 and 1116 micrographs were combined for processing. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |