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- EMDB-39107: SARS-CoV-2 DMV nsp3-4 pore complex (full-pore) -

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Basic information

Entry
Database: EMDB / ID: EMD-39107
TitleSARS-CoV-2 DMV nsp3-4 pore complex (full-pore)
Map datalocal resolution map, processed by relion_postprocess
Sample
  • Complex: SARS-CoV-2 nsp3-4 pore complex
    • Protein or peptide: Papain-like protease nsp3
    • Protein or peptide: Non-structural protein 4
KeywordsDouble 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 / 5'-3' DNA helicase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
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 / Lipocalin signature. / (+) 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 / 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. / : / 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 3Ecto domain profile. / : / 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
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 4.9 Å
AuthorsHuang YX / Zhong LJ / Zhang WX / Ni T
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: To Be Published
Title: Molecular Architecture of Coronavirus Double Membrane Vesicle Pore Complex
Authors: Huang YX / Ni T
History
DepositionFeb 10, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39107.png

Downloads & links

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Map

FileDownload / File: emd_39107.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map, processed by relion_postprocess
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 288 pix.
= 452.448 Å		1.57 Å/pix.
x 288 pix.
= 452.448 Å		1.57 Å/pix.
x 288 pix.
= 452.448 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.3609886 - 2.9449346
Average (Standard dev.)-0.00000045516433 (±0.08809528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 452.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39107_msk_1.map
Projections & Slices
AxesZYX

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Additional map: local refinement map focused on nsp3NTD domain

Fileemd_39107_additional_1.map
Annotationlocal refinement map focused on nsp3NTD domain
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39107_half_map_1.map
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Half map: #1

Fileemd_39107_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 nsp3-4 pore complex

EntireName: SARS-CoV-2 nsp3-4 pore complex
Components
  • Complex: SARS-CoV-2 nsp3-4 pore complex
    • Protein or peptide: Papain-like protease nsp3
    • Protein or peptide: Non-structural protein 4

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Supramolecule #1: SARS-CoV-2 nsp3-4 pore complex

SupramoleculeName: SARS-CoV-2 nsp3-4 pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Papain-like protease nsp3

MacromoleculeName: Papain-like protease nsp3 / 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 weightTheoretical: 217.471188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Non-structural protein 4

MacromoleculeName: Non-structural protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 56.229582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
10.0 mMTris-HClTrisTris hydrochloride
1.0 mMEDTAEthylenediaminetetraacetic acidEthylenediaminetetraacetic acid

Details: 150mM NaCl, 10mM Tris-HCl, 1mM EDTA
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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: 6.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 4746 / Number images used: 598699 / Reference model: EMD-11514 / Software - Name: emClarity (ver. v1.6.2)
Final 3D classificationSoftware - Name: RELION (ver. v4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. v4)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v4) / Number subtomograms used: 30607
DetailsFalcon 4i Selectris X energy filter
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8f2e

source_name: PDB, initial_model_type: experimental model

6wrh

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF Chimera (ver. 1.16)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8yax:
SARS-CoV-2 DMV nsp3-4 pore complex (full-pore)

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