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- EMDB-7063: Cryo-electron microscopy structure of porcine delta coronavirus s... -

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Basic information

Entry
Database: EMDB / ID: EMD-7063
TitleCryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state
Map dataDelta coronavirus spike protein in the pre-fusion state
Sample
  • Complex: Porcine delta coronavirus spike trimer in the pre-fusion state
    • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / host cell membrane / endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesDeltacoronavirus PDCoV/USA/Ohio137/2014
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShang J / Zheng Y / Yang Y / Liu C / Geng Q / Tai W / Du L / Zhou Y / Zhang W / Li F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089728 United States
University of Minnesota United States
CitationJournal: J Virol / Year: 2018
Title: Cryo-Electron Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion State.
Authors: Jian Shang / Yuan Zheng / Yang Yang / Chang Liu / Qibin Geng / Wanbo Tai / Lanying Du / Yusen Zhou / Wei Zhang / Fang Li /
Abstract: Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here, we ...Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at 3.3-Å resolution. The trimeric protein contains three receptor-binding S1 subunits that tightly pack into a crown-like structure and three membrane fusion S2 subunits that form a stalk. Each S1 subunit contains two domains, an N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD). PdCoV S1-NTD has the same structural fold as alpha- and betacoronavirus S1-NTDs as well as host galectins, and it recognizes sugar as its potential receptor. PdCoV S1-CTD has the same structural fold as alphacoronavirus S1-CTDs, but its structure differs from that of betacoronavirus S1-CTDs. PdCoV S1-CTD binds to an unidentified receptor on host cell surfaces. PdCoV S2 is locked in the prefusion conformation by structural restraint of S1 from a different monomeric subunit. PdCoV spike possesses several structural features that may facilitate immune evasion by the virus, such as its compact structure, concealed receptor-binding sites, and shielded critical epitopes. Overall, this study reveals that deltacoronavirus spikes are structurally and evolutionally more closely related to alphacoronavirus spikes than to betacoronavirus spikes; it also has implications for the receptor recognition, membrane fusion, and immune evasion by deltacoronaviruses as well as coronaviruses in general. IMPORTANCE In this study, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at a 3.3-Å resolution. This is the first atomic structure of a spike protein from the deltacoronavirus genus, which is divergent in amino acid sequences from the well-studied alpha- and betacoronavirus spike proteins. Here, we described the overall structure of the PdCoV spike and the detailed structure of each of its structural elements. Moreover, we analyzed the functions of each of the structural elements. Based on the structures and functions of these structural elements, we discussed the evolution of PdCoV spike protein in relation to the spike proteins from other coronavirus genera. This study combines the structure, function, and evolution of PdCoV spike protein and provides many insights into its receptor recognition, membrane fusion, and immune evasion.
History
DepositionOct 4, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseOct 25, 2017-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0468
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0468
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6b7n
  • Surface level: 0.0468
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7063.png

Downloads & links

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Map

FileDownload / File: emd_7063.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDelta coronavirus spike protein in the pre-fusion state
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.0468 / Movie #1: 0.0468
Minimum - Maximum-0.028543813 - 0.13612749
Average (Standard dev.)0.0001462406 (±0.005408163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0290.1360.000

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Supplemental data

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Sample components

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Entire : Porcine delta coronavirus spike trimer in the pre-fusion state

EntireName: Porcine delta coronavirus spike trimer in the pre-fusion state
Components
  • Complex: Porcine delta coronavirus spike trimer in the pre-fusion state
    • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Porcine delta coronavirus spike trimer in the pre-fusion state

SupramoleculeName: Porcine delta coronavirus spike trimer in the pre-fusion state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Deltacoronavirus PDCoV/USA/Ohio137/2014
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Deltacoronavirus PDCoV/USA/Ohio137/2014
Molecular weightTheoretical: 122.277266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FADDLLDLLT FPGAHRFLHK PTRNSSSLYS RANNNFDVGV LPGYPTKNVN LFSPLTNSTL PINGLHRSYQ PLMLNCLTKI TNHTLSMYL LPSEIQTYSC GGAMVKYQTH DAVRIILDLT ATDHISVEVV GQHGENYVFV CSEQFNYTTA LHNSTFFSLN S ELYCFTNN ...String:
FADDLLDLLT FPGAHRFLHK PTRNSSSLYS RANNNFDVGV LPGYPTKNVN LFSPLTNSTL PINGLHRSYQ PLMLNCLTKI TNHTLSMYL LPSEIQTYSC GGAMVKYQTH DAVRIILDLT ATDHISVEVV GQHGENYVFV CSEQFNYTTA LHNSTFFSLN S ELYCFTNN TYLGILPPDL TDFTVYRTGQ FYANGYLLGT LPITVNYVRL YRGHLSANSA HFALANLTDT LITLTNTTIS QI TYCDKSV VDSIACQRSS HEVEDGFYSD PKSAVRARQR TIVTLPKLPE LEVVQLNISA HMDFGEARLD SVTINGNTSY CVT KPYFRL ETNFMCTGCT MNLRTDTCSF DLSAVNNGMS FSQFCLSTES GACEMKIIVT YVWNYLLRQR LYVTAVEGQT HTGT TSVHA TDTSSVITDV CTDYTIYGVS GTGIIKPSDL LLHNGIAFTS PTGELYAFKN ITTGKTLQVL PCETPSQLIV INNTV VGAI TSSNSTENNR FTTTIVTPTF FYSTNATTFN CTKPVLSYGP ISVCSDGAIV GISTLQNTRP SIVSLYDGEV EIPSAF SLS VQTEYLQVQA EQVIVDCPQY VCNGNSRCLQ LLAQYTSACS NIEAALHSSA QLDSREIINM FKTSTQSLQL ANITNFK GD YNFSSILTTR IGGRSAIEDL LFNKVVTSGL GTVDQDYKSC SRDMAIADLV CSQYYNGIMV LPGVVDAEKM AMYTGSLT G AMVFGGLTAA AAIPFATAVQ ARLNYVALQT NVLQENQKIL AESFNQAVGN ISLALSSVND AIQQTSEALN TVAIAIKKI QTVVNQQGEA LSHLTAQLSN NFQAISTSIQ DIYNRLEEVE ANQQVDRLIT GRLAALNAYV TQLLNQMSQI RQSRLLAQQK INECVKSQS SRYGFCGNGT HIFSLTQTAP NGIFFMHAVL VPNKFTRVNA SAGICVDNTR GYSLQPQLIL YQFNNSWRVT P RNMYEPRL PRQADFIQLT DCSVTFYNTT AANLPNIIPD IIDVNQTVSD IIDNLPTATP PQWDVGIYNN TILNLTVEIN DL QERSKNL SQIADRLQNY IDNVDIKQIE DKIEEILSKI YHIENEIARI KKLIGEIGGG GSHHHHHHHH

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.2
GridModel: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87002

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