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- EMDB-39109: SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-39109
TitleSARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)
Map datalocal resolution map
Sample
  • Complex: SARS-CoV-2 DMV 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 / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / 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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / 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 / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 Interface domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) 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, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / : / Coronavirus 3Ecto domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / : / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Peptidase family C16 domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 4.2 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: Nature / Year: 2024
Title: Molecular architecture of coronavirus double-membrane vesicle pore complex.
Authors: Yixin Huang / Tongyun Wang / Lijie Zhong / Wenxin Zhang / Yu Zhang / Xiulian Yu / Shuofeng Yuan / Tao Ni /
Abstract: Coronaviruses remodel the intracellular host membranes during replication, forming double-membrane vesicles (DMVs) to accommodate viral RNA synthesis and modifications. SARS-CoV-2 non-structural ...Coronaviruses remodel the intracellular host membranes during replication, forming double-membrane vesicles (DMVs) to accommodate viral RNA synthesis and modifications. SARS-CoV-2 non-structural protein 3 (nsp3) and nsp4 are the minimal viral components required to induce DMV formation and to form a double-membrane-spanning pore, essential for the transport of newly synthesized viral RNAs. The mechanism of DMV pore complex formation remains unknown. Here we describe the molecular architecture of the SARS-CoV-2 nsp3-nsp4 pore complex, as resolved by cryogenic electron tomography and subtomogram averaging in isolated DMVs. The structures uncover an unexpected stoichiometry and topology of the nsp3-nsp4 pore complex comprising 12 copies each of nsp3 and nsp4, organized in 4 concentric stacking hexamer rings, mimicking a miniature nuclear pore complex. The transmembrane domains are interdigitated to create a high local curvature at the double-membrane junction, coupling double-membrane reorganization with pore formation. The ectodomains form extensive contacts in a pseudo-12-fold symmetry, belting the pore complex from the intermembrane space. A central positively charged ring of arginine residues coordinates the putative RNA translocation, essential for virus replication. Our work establishes a framework for understanding DMV pore formation and RNA translocation, providing a structural basis for the development of new antiviral strategies to combat coronavirus infection.
History
DepositionFeb 11, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39109.png

Downloads & links

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Map

FileDownload / File: emd_39109.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map
Projections & slices

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.571 Å
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Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.3199544 - 4.757655
Average (Standard dev.)0.0000011922106 (±0.117278196)
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_39109_msk_1.map
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Half map: #2

Fileemd_39109_half_map_1.map
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Half map: #1

Fileemd_39109_half_map_2.map
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Sample components

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

EntireName: SARS-CoV-2 DMV nsp3-4 pore complex
Components
  • Complex: SARS-CoV-2 DMV 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 DMV nsp3-4 pore complex

SupramoleculeName: SARS-CoV-2 DMV 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 chloride
10.0 mMTris-HClTris hydrochloride
1.0 mMEDTAEthylenediaminetetraacetic 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
SoftwareName: SerialEM
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v4) / Number subtomograms used: 113163
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)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF Chimera (ver. 1.16)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8yb5:
SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)

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