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- EMDB-21399: Porcine epidemic diarrhea virus (PEDV) spike protein bound to pol... -

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Basic information

Entry
Database: EMDB / ID: EMD-21399
TitlePorcine epidemic diarrhea virus (PEDV) spike protein bound to polyclonal Fab sample 1, side-binding Fab
Map data
Sample
  • Complex: Porcine epidemic diarrhea virus spike protein bound to polyclonal Fab from a PEDV infected pig.
    • Protein or peptide: Porcine epidemic diarrhea virus (PEDV) spike protein
Biological speciesPorcine epidemic diarrhea virus
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsKirchdoerfer RN / Martini O / Sewall LM / Bangaru S / 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: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21399.png

Downloads & links

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Map

FileDownload / File: emd_21399.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.100739084 - 0.3238301
Average (Standard dev.)-0.004624575 (±0.03226441)
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-0.1010.324-0.005

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Supplemental data

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Mask #1

Fileemd_21399_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_21399_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_21399_half_map_2.map
Projections & Slices
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Sample components

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Entire : Porcine epidemic diarrhea virus spike protein bound to polyclonal...

EntireName: Porcine epidemic diarrhea virus spike protein bound to polyclonal Fab from a PEDV infected pig.
Components
  • Complex: Porcine epidemic diarrhea virus spike protein bound to polyclonal Fab from a PEDV infected pig.
    • Protein or peptide: Porcine epidemic diarrhea virus (PEDV) spike protein

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Supramolecule #1: Porcine epidemic diarrhea virus spike protein bound to polyclonal...

SupramoleculeName: Porcine epidemic diarrhea virus spike protein bound to polyclonal Fab from a PEDV infected pig.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed in insect cells using a baculovirus vector. Fab produced by proteolytic digest of polyclonal IgG.
Source (natural)Organism: Porcine epidemic diarrhea virus / Strain: 13-019349
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9

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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 NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QG VNSTWYC AGQHPTASGV HGIFVSHIRG GHGFEIGISQ EPFDPSGYQL YLHKATNGNT NAT ARLRIC QFPSIKTLGP TANNDVTTGR NCLFNKAIPA HMSEHSVVGI TWDNDRVTVF SDKI YYFYF ...String:
LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QG VNSTWYC AGQHPTASGV HGIFVSHIRG GHGFEIGISQ EPFDPSGYQL YLHKATNGNT NAT ARLRIC QFPSIKTLGP TANNDVTTGR NCLFNKAIPA HMSEHSVVGI TWDNDRVTVF SDKI YYFYF KNDWSRVATK CYNSGGCAMQ YVYEPTYYML NVTSAGEDGI SYQPCTANCI GYAAN VFAT EPNGHIPEGF SFNNWFLLSN DSTLVHGKVV SNQPLLVNCL LAIPKIYGLG QFFSFN QTI DGVCNGAAVQ RAPEALRFNI NDISVILAEG SIVLHTALGT NFSFVCSNSS NPHLATF AI PLGATQVPYY CFLKVDTYNS TVYKFLAVLP PTVREIVITK YGDVYVNGFG YLHLGLLD A VTINFTGHGT DDDVSGFWTI ASTNFVDALI EVQGTAIQRI LYCDDPVSQL KCSQVAFDL DDGFYTISSR NLLSHEQPIS FVTLPSFNDH SFVNITVSAS FGGHSGANLI ASDTTINGFS SFCVDTRQF TISLFYNVTN SYGYVSKSQD SNCPFTLQSV NDYLSFSKFC VSTSLLASAC T IDLFGYPE FGSGVKFTSL YFQFTKGELI TGTPKPFEGV TDVSFMTLDV CTKYTIYGFK GE GIITLTN SSFLAGVYYT SDSGQLLAFK NVTSGAVYSV TPCSFSEQAA YVDDDIVGVI SSL SSSTFN STRELPGFFY HSNDGSNCTE PVLVYSNIGV CKSGSIGYVP SQSGQVKIAP TVTG NISIP TNFSMSIRTE YLQLYNTPVS VDCATYVCNG NSRCKQLLTQ YTAACKTIES ALQLS ARLE SVEVNSMLTI SDEALQLATI SSFNGDGYNF TNVLGVSVYD PASGRVVQKR SFIEDL LFN KVVTNGLGTV DEDYKRCSNG RSVADLVCAQ YYSGVMVLPG VVDAEKLHMY SASLIGG MV LGGFTSAAAL PFSYAVQARL NYLALQTDVL QRNQQLLAES FNSAIGNITS AFESVKEA I SQTSKGLNTV AHALTKVQEV VNSQGAALTQ LTVQLQHNFQ AISSSIDDIY SRLDILSAD AQVDRLITGR LSALNAFVAQ TLTKYTEVQA SRKLAQQKVN ECVKSQSQRY GFCGGDGEHI FSLVQAAPQ GLLFLHTVLV PSDFVDVIAI AGLCVNDEIA LTLREPGLVL FTHELQNHTA T EYFVSSRR MFEPRKPTVS DFVQIESCVV TYVNLTRDQL PDVIPDYIDV NKTLDEILAS LP NRTGPSL PLDVFNATYL NLTGEIADLE QRSESLRNTT EELQSLIYNI NNTLVDLEWL NRV ETGSGY IPEAPRDGQA YVRKDGEWVL 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

Concentration0.06 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5szs

Final reconstructionNumber classes used: 50 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 4552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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