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Yorodumi- EMDB-39112: SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C3 symmetry) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39112 | |||||||||
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Title | SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C3 symmetry) | |||||||||
Map data | local resolution map | |||||||||
Sample |
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Keywords | Double membrane vesicle / pore complex / nsp3 / nsp4 / RNA transport / 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 | subtomogram averaging / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Huang YX / Zhong LJ / Zhang WX / Ni T | |||||||||
Funding support | Hong Kong, 1 items
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Citation | Journal: To Be Published Title: Molecular Architecture of Coronavirus Double Membrane Vesicle Pore Complex Authors: Huang YX / Ni T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39112.map.gz | 51.7 MB | EMDB map data format | |
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Header (meta data) | emd-39112-v30.xml emd-39112.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39112_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_39112.png | 187.9 KB | ||
Masks | emd_39112_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-39112.cif.gz | 7.7 KB | ||
Others | emd_39112_half_map_1.map.gz emd_39112_half_map_2.map.gz | 44.7 MB 44.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39112 | HTTPS FTP |
-Validation report
Summary document | emd_39112_validation.pdf.gz | 889.6 KB | Display | EMDB validaton report |
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Full document | emd_39112_full_validation.pdf.gz | 889.2 KB | Display | |
Data in XML | emd_39112_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_39112_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39112 | HTTPS FTP |
-Related structure data
Related structure data | 8yb7MC 8yaxC 8yb5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39112.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.571 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_39112_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39112_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39112_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 nsp3-4 pore complex
Entire | Name: SARS-CoV-2 nsp3-4 pore complex |
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Components |
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-Supramolecule #1: SARS-CoV-2 nsp3-4 pore complex
Supramolecule | Name: SARS-CoV-2 nsp3-4 pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Papain-like protease nsp3
Macromolecule | Name: Papain-like protease nsp3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 217.471188 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: APTKVTFGDD TVIEVQGYKS VNITFELDER IDKVLNEKCS AYTVELGTEV NEFACVVADA VIKTLQPVSE LLTPLGIDLD EWSMATYYL FDESGEFKLA SHMYCSFYPP DEDEEEGDCE EEEFEPSTQY EYGTEDDYQG KPLEFGATSA ALQPEEEQEE D WLDDDSQQ ...String: APTKVTFGDD TVIEVQGYKS VNITFELDER IDKVLNEKCS AYTVELGTEV NEFACVVADA VIKTLQPVSE LLTPLGIDLD EWSMATYYL FDESGEFKLA SHMYCSFYPP DEDEEEGDCE EEEFEPSTQY EYGTEDDYQG KPLEFGATSA ALQPEEEQEE D WLDDDSQQ TVGQQDGSED NQTTTIQTIV EVQPQLEMEL TPVVQTIEVN SFSGYLKLTD NVYIKNADIV EEAKKVKPTV VV NAANVYL KHGGGVAGAL NKATNNAMQV ESDDYIATNG PLKVGGSCVL SGHNLAKHCL HVVGPNVNKG EDIQLLKSAY ENF NQHEVL LAPLLSAGIF GADPIHSLRV CVDTVRTNVY LAVFDKNLYD KLVSSFLEMK SEKQVEQKIA EIPKEEVKPF ITES KPSVE QRKQDDKKIK ACVEEVTTTL EETKFLTENL LLYIDINGNL HPDSATLVSD IDITFLKKDA PYIVGDVVQE GVLTA VVIP TKKAGGTTEM LAKALRKVPT DNYITTYPGQ GLNGYTVEEA KTVLKKCKSA FYILPSIISN EKQEILGTVS WNLREM LAH AEETRKLMPV CVETKAIVST IQRKYKGIKI QEGVVDYGAR FYFYTSKTTV ASLINTLNDL NETLVTMPLG YVTHGLN LE EAARYMRSLK VPATVSVSSP DAVTAYNGYL TSSSKTPEEH FIETISLAGS YKDWSYSGQS TQLGIEFLKR GDKSVYYT S NPTTFHLDGE VITFDNLKTL LSLREVRTIK VFTTVDNINL HTQVVDMSMT YGQQFGPTYL DGADVTKIKP HNSHEGKTF YVLPNDDTLR VEAFEYYHTT DPSFLGRYMS ALNHTKKWKY PQVNGLTSIK WADNNCYLAT ALLTLQQIEL KFNPPALQDA YYRARAGEA ANFCALILAY CNKTVGELGD VRETMSYLFQ HANLDSCKRV LNVVCKTCGQ QQTTLKGVEA VMYMGTLSYE Q FKKGVQIP CTCGKQATKY LVQQESPFVM MSAPPAQYEL KHGTFTCASE YTGNYQCGHY KHITSKETLY CIDGALLTKS SE YKGPITD VFYKENSYTT TIKPVTYKLD GVVCTEIDPK LDNYYKKDNS YFTEQPIDLV PNQPYPNASF DNFKFVCDNI KFA DDLNQL TGYKKPASRE LKVTFFPDLN GDVVAIDYKH YTPSFKKGAK LLHKPIVWHV NNATNKATYK PNTWCIRCLW STKP VETSN SFDVLKSEDA QGMDNLACED LKPVSEEVVE NPTIQKDVLE CNVKTTEVVG DIILKPANNS LKITEEVGHT DLMAA YVDN SSLTIKKPNE LSRVLGLKTL ATHGLAAVNS VPWDTIANYA KPFLNKVVST TTNIVTRCLN RVCTNYMPYF FTLLLQ LCT FTRSTNSRIK ASMPTTIAKN TVKSVGKFCL EASFNYLKSP NFSKLINIII WFLLLSVCLG SLIYSTAALG VLMSNLG MP SYCTGYREGY LNSTNVTIAT YCTGSIPCSV CLSGLDSLDT YPSLETIQIT ISSFKWDLTA FGLVAEWFLA YILFTRFF Y VLGLAAIMQL FFSYFAVHFI SNSWLMWLII NLVQMAPISA MVRMYIFFAS FYYVWKSYVH VVDGCNSSTC MMCYKRNRA TRVECTTIVN GVRRSFYVYA NGGKGFCKLH NWNCVNCDTF CAGSTFISDE VARDLSLQFK RPINPTDQSS YIVDSVTVKN GSIHLYFDK AGQKTYERHS LSHFVNLDNL RANNTKGSLP INVIVFDGKS KCEESSAKSA SVYYSQLMCQ PILLLDQALV S DVGDSAEV AVKMFDAYVN TFSSTFNVPM EKLKTLVATA EAELAKNVSL DNVLSTFISA ARQGFVDSDV ETKDVVECLK LS HQSDIEV TGDSCNNYML TYNKVENMTP RDLGACIDCS ARHINAQVAK SHNIALIWNV KDFMSLSEQL RKQIRSAAKK NNL PFKLTC ATTRQVVNVV TTKIALKGG UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: Non-structural protein 4
Macromolecule | Name: Non-structural protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 56.229582 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KIVNNWLKQL IKVTLVFLFV AAIFYLITPV HVMSKHTDFS SEIIGYKAID GGVTRDIAST DTCFANKHAD FDTWFSQRGG SYTNDKACP LIAAVITREV GFVVPGLPGT ILRTTNGDFL HFLPRVFSAV GNICYTPSKL IEYTDFATSA CVLAAECTIF K DASGKPVP ...String: KIVNNWLKQL IKVTLVFLFV AAIFYLITPV HVMSKHTDFS SEIIGYKAID GGVTRDIAST DTCFANKHAD FDTWFSQRGG SYTNDKACP LIAAVITREV GFVVPGLPGT ILRTTNGDFL HFLPRVFSAV GNICYTPSKL IEYTDFATSA CVLAAECTIF K DASGKPVP YCYDTNVLEG SVAYESLRPD TRYVLMDGSI IQFPNTYLEG SVRVVTTFDS EYCRHGTCER SEAGVCVSTS GR WVLNNDY YRSLPGVFCG VDAVNLLTNM FTPLIQPIGA LDISASIVAG GIVAIVVTCL AYYFMRFRRA FGEYSHVVAF NTL LFLMSF TVLCLTPVYS FLPGVYSVIY LYLTFYLTND VSFLAHIQWM VMFTPLVPFW ITIAYIICIS TKHFYWFFSN YLKR RVVFN GVSFSTFEEA ALCTFLLNKE MYLKLRSDVL LPLTQYNRYL ALYNKYKYFS GAMDTTSYRE AACCHLAKAL NDFSN SGSD VLYQPPQTSI TSAVLQ UniProtKB: Replicase polyprotein 1ab |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 150mM NaCl, 10mM Tris-HCl, 1mM EDTA | ||||||||||||
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Grid | Model: EMS Lacey Carbon / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.0 e/Å2 Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -51 ...Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -51 degree to 51 degree (or -60 to 60) at 3 degree increments and an exposure dose of 3 e/A2 per image. The total dose was 105 or 123 e/A2. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Software | Name: UCSF Chimera (ver. 1.16) |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8yb7: |