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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
Sample
  • Complex: Porcine epidemic diarrhea virus spike protein
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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, Alphacoronavirus / 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 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)
Voxel sizeX=Y=Z: 1.15 Å
Density
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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Mask #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
Components
  • Complex: Porcine epidemic diarrhea virus spike protein
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID

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Supramolecule #1: Porcine epidemic diarrhea virus spike protein

SupramoleculeName: Porcine epidemic diarrhea virus spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Recombinantly expressed in insect cells using a baculovirus vector.
Source (natural)Organism: Porcine epidemic diarrhea virus / Strain: 13-019349
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9
Molecular weightExperimental: 600 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porcine epidemic diarrhea virus
Molecular weightTheoretical: 148.463656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QGVNSTWYCA GQHPTASGVH GIFVSHIRGG HGFEIGISQE PFDPSGYQL YLHKATNGNT NATARLRICQ FPSIKTLGPT ANNDVTTGRN CLFNKAIPAH MSEHSVVGIT WDNDRVTVFS D KIYYFYFK ...String:
LPQDVTRCSA NTNFRRFFSK FNVQAPAVVV LGGYLPIGEN QGVNSTWYCA GQHPTASGVH GIFVSHIRGG HGFEIGISQE PFDPSGYQL YLHKATNGNT NATARLRICQ FPSIKTLGPT ANNDVTTGRN CLFNKAIPAH MSEHSVVGIT WDNDRVTVFS D KIYYFYFK NDWSRVATKC YNSGGCAMQY VYEPTYYMLN VTSAGEDGIS YQPCTANCIG YAANVFATEP NGHIPEGFSF NN WFLLSND STLVHGKVVS NQPLLVNCLL AIPKIYGLGQ FFSFNQTIDG VCNGAAVQRA PEALRFNIND ISVILAEGSI VLH TALGTN FSFVCSNSSN PHLATFAIPL GATQVPYYCF LKVDTYNSTV YKFLAVLPPT VREIVITKYG DVYVNGFGYL HLGL LDAVT INFTGHGTDD DVSGFWTIAS TNFVDALIEV QGTAIQRILY CDDPVSQLKC SQVAFDLDDG FYTISSRNLL SHEQP ISFV TLPSFNDHSF VNITVSASFG GHSGANLIAS DTTINGFSSF CVDTRQFTIS LFYNVTNSYG YVSKSQDSNC PFTLQS VND YLSFSKFCVS TSLLASACTI DLFGYPEFGS GVKFTSLYFQ FTKGELITGT PKPFEGVTDV SFMTLDVCTK YTIYGFK GE GIITLTNSSF LAGVYYTSDS GQLLAFKNVT SGAVYSVTPC SFSEQAAYVD DDIVGVISSL SSSTFNSTRE LPGFFYHS N DGSNCTEPVL VYSNIGVCKS GSIGYVPSQS GQVKIAPTVT GNISIPTNFS MSIRTEYLQL YNTPVSVDCA TYVCNGNSR CKQLLTQYTA ACKTIESALQ LSARLESVEV NSMLTISDEA LQLATISSFN GDGYNFTNVL GVSVYDPASG RVVQKRSFIE DLLFNKVVT NGLGTVDEDY KRCSNGRSVA DLVCAQYYSG VMVLPGVVDA EKLHMYSASL IGGMVLGGFT SAAALPFSYA V QARLNYLA LQTDVLQRNQ QLLAESFNSA IGNITSAFES VKEAISQTSK GLNTVAHALT KVQEVVNSQG AALTQLTVQL QH NFQAISS SIDDIYSRLD ILSADAQVDR LITGRLSALN AFVAQTLTKY TEVQASRKLA QQKVNECVKS QSQRYGFCGG DGE HIFSLV QAAPQGLLFL HTVLVPSDFV DVIAIAGLCV NDEIALTLRE PGLVLFTHEL QNHTATEYFV SSRRMFEPRK PTVS DFVQI ESCVVTYVNL TRDQLPDVIP DYIDVNKTLD EILASLPNRT GPSLPLDVFN ATYLNLTGEI ADLEQRSESL RNTTE ELQS LIYNINNTLV DLEWLNRVET GSGYIPEAPR DGQAYVRKDG EWVLLSTFLE NLYFQGGHHH HHHAWSHPQF EK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / 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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Macromolecule #6: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 6 / Number of copies: 6 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
PALMITOLEIC ACID / Palmitoleic acid

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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

Concentration1.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
25.0 mMTris
150.0 mMsodium chloride
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMax: 100.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-64 / Number grids imaged: 1 / Average exposure time: 12.8 sec. / Average electron dose: 54.9 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19436
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: SGD initial model generation
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 19436
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5szs


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6vv5:
Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein

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