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

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Entry
Database: EMDB / ID: 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
SamplePorcine delta coronavirus spike trimer in the pre-fusion state:
Spike protein / ligand
Function / homologyCoronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / Coronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / integral component of membrane / Spike protein
Function and homology information
SourceDeltacoronavirus PDCoV/USA/Ohio137/2014
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsShang J / Zheng Y / Yang Y / Liu C / Geng Q / Tai W / Du L / Zhou Y / Zhang W / Li F
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.
Validation ReportPDB-ID: 6b7n

SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Dec 6, 2017

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Structure visualization

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

Downloads & links

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Map

Fileemd_7063.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.0468 (by author), 0.0468 (movie #1):
Minimum - Maximum-0.028543813 - 0.13612749
Average (Standard dev.)0.0001462406 (0.005408163)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 3

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Component #1: protein, Porcine delta coronavirus spike trimer in the pre-fusion...

ProteinName: Porcine delta coronavirus spike trimer in the pre-fusion state
Recombinant expression: No
SourceSpecies: Deltacoronavirus PDCoV/USA/Ohio137/2014
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Spike protein

ProteinName: Spike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 122.277266 kDa
SourceSpecies: Deltacoronavirus PDCoV/USA/Ohio137/2014
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 57 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.35 mg/ml / pH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 87002
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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