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- EMDB-21397: Porcine epidemic diarrhea virus (PEDV) spike protein, N-terminal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21397
TitlePorcine epidemic diarrhea virus (PEDV) spike protein, N-terminal domain deletion, expressed in Sf9 cells and negatively stained
Map data
Sample
  • Complex: Porcine epidemic diarrhea virus spike protein with a deletion of the N-terminal domain 0
    • Protein or peptide: Porcine epidemic diarrhea virus (PEDV) spike protein
Biological speciesPorcine epidemic diarrhea virus
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsKirchdoerfer RN / Martini O / 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: 0.165
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.165
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21397.png

Downloads & links

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Map

FileDownload / File: emd_21397.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 96 pix.
= 393.6 Å		4.1 Å/pix.
x 96 pix.
= 393.6 Å		4.1 Å/pix.
x 96 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.165 / Movie #1: 0.165
Minimum - Maximum-0.083587185 - 0.4614907
Average (Standard dev.)8.627674e-05 (±0.026901763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0840.4610.000

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Supplemental data

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Mask #1

Fileemd_21397_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_21397_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_21397_half_map_2.map
Projections & Slices
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Sample components

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Entire : Porcine epidemic diarrhea virus spike protein with a deletion of ...

EntireName: Porcine epidemic diarrhea virus spike protein with a deletion of the N-terminal domain 0
Components
  • Complex: Porcine epidemic diarrhea virus spike protein with a deletion of the N-terminal domain 0
    • Protein or peptide: Porcine epidemic diarrhea virus (PEDV) spike protein

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Supramolecule #1: Porcine epidemic diarrhea virus spike protein with a deletion of ...

SupramoleculeName: Porcine epidemic diarrhea virus spike protein with a deletion of the N-terminal domain 0
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed in Sf9 cells using baculovirus
Source (natural)Organism: Porcine epidemic diarrhea virus / Strain: 13-019349
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 / Recombinant plasmid: pFastBac
Molecular weightExperimental: 600 KDa

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Macromolecule #1: Porcine epidemic diarrhea virus (PEDV) spike protein

MacromoleculeName: Porcine epidemic diarrhea virus (PEDV) spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LPQDVTRCSA NTNFRTANCI GYAANVFATE PNGHIPEGFS FN NWFLLSN DSTLVHGKVV SNQPLLVNCL LAIPKIYGLG QFFSFNQTID GVCNGAAVQR APE ALRFNI NDISVILAEG SIVLHTALGT NFSFVCSNSS NPHLATFAIP LGATQVPYYC FLKV DTYNS ...String:
LPQDVTRCSA NTNFRTANCI GYAANVFATE PNGHIPEGFS FN NWFLLSN DSTLVHGKVV SNQPLLVNCL LAIPKIYGLG QFFSFNQTID GVCNGAAVQR APE ALRFNI NDISVILAEG SIVLHTALGT NFSFVCSNSS NPHLATFAIP LGATQVPYYC FLKV DTYNS TVYKFLAVLP PTVREIVITK YGDVYVNGFG YLHLGLLDAV TINFTGHGTD DDVSG FWTI ASTNFVDALI EVQGTAIQRI LYCDDPVSQL KCSQVAFDLD DGFYTISSRN LLSHEQ PIS FVTLPSFNDH SFVNITVSAS FGGHSGANLI ASDTTINGFS SFCVDTRQFT ISLFYNV TN SYGYVSKSQD SNCPFTLQSV NDYLSFSKFC VSTSLLASAC TIDLFGYPEF GSGVKFTS L YFQFTKGELI TGTPKPFEGV TDVSFMTLDV CTKYTIYGFK GEGIITLTNS SFLAGVYYT SDSGQLLAFK NVTSGAVYSV TPCSFSEQAA YVDDDIVGVI SSLSSSTFNS TRELPGFFYH SNDGSNCTE PVLVYSNIGV CKSGSIGYVP SQSGQVKIAP TVTGNISIPT NFSMSIRTEY L QLYNTPVS VDCATYVCNG NSRCKQLLTQ YTAACKTIES ALQLSARLES VEVNSMLTIS DE ALQLATI SSFNGDGYNF TNVLGVSVYD PASGRVVQKR SFIEDLLFNK VVTNGLGTVD EDY KRCSNG RSVADLVCAQ YYSGVMVLPG VVDAEKLHMY SASLIGGMVL GGFTSAAALP FSYA VQARL NYLALQTDVL QRNQQLLAES FNSAIGNITS AFESVKEAIS QTSKGLNTVA HALTK VQEV VNSQGAALTQ LTVQLQHNFQ AISSSIDDIY SRLDILSADA QVDRLITGRL SALNAF VAQ TLTKYTEVQA SRKLAQQKVN ECVKSQSQRY GFCGGDGEHI FSLVQAAPQG LLFLHTV LV PSDFVDVIAI AGLCVNDEIA LTLREPGLVL FTHELQNHTA TEYFVSSRRM FEPRKPTV S DFVQIESCVV TYVNLTRDQL PDVIPDYIDV NKTLDEILAS LPNRTGPSLP LDVFNATYL NLTGEIADLE QRSESLRNTT EELQSLIYNI NNTLVDLEWL NRVETGSGYI PEAPRDGQAY VRKDGEWVL LSTFLENLYF QGGHHHHHHA WSHPQFEK

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
25.0 mMTris
150.0 mMsodium chloride
StainingType: NEGATIVE / Material: Uranyl formate
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-64 / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18070
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5szs


Details: SGD initial model generation
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 18070
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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