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- EMDB-21391: Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike... -

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Basic information

Entry
Database: EMDB / ID: EMD-21391
TitleCryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein
Map data
SamplePorcine epidemic diarrhea virus spike protein:
Spike glycoproteinSpike protein / (ligand) x 2
Function / homology
Function and homology information


: / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / integral component of membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S2 / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKirchdoerfer RN / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127521 United States
CitationJournal: Structure / Year: 2021
Title: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein.
Authors: Robert N Kirchdoerfer / Mahesh Bhandari / Olnita Martini / Leigh M Sewall / Sandhya Bangaru / Kyoung-Jin Yoon / Andrew B Ward /
Abstract: Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a ...Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
History
DepositionFeb 17, 2020-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 26, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vv5
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21391.png

Downloads & links

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Map

FileDownload / File: emd_21391.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å		1.15 Å/pix.
x 280 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.11378142 - 0.18057886
Average (Standard dev.)7.580524e-05 (±0.0069649033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z322.000322.000322.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1140.1810.000

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Supplemental data

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Segmentation: #1

Fileemd_21391_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map

Fileemd_21391_half_map_1.map
AnnotationFirst half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_21391_half_map_2.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire Porcine epidemic diarrhea virus spike protein

EntireName: Porcine epidemic diarrhea virus spike protein
Details: Recombinantly expressed in insect cells using a baculovirus vector.
Number of Components: 4

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Component #1: protein, Porcine epidemic diarrhea virus spike protein

ProteinName: Porcine epidemic diarrhea virus spike protein
Details: Recombinantly expressed in insect cells using a baculovirus vector.
Recombinant expression: No
MassExperimental: 600 kDa
SourceSpecies: Porcine epidemic diarrhea virus / Strain: 13-019349
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Strain: Sf9

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 148.463656 kDa
SourceSpecies: Porcine epidemic diarrhea virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #4: ligand, PALMITOLEIC ACID

LigandName: PALMITOLEIC ACID / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.254408 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.3 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 54.9 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD / Defocus: 600.0 - 1400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: ( - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C3 (3 fold cyclic) / Number of Projections: 19436
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5SZS

5szs


Chain ID: A
Output model

6vv5

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