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- EMDB-19017: S1B domain of the PDCoV spike glycoprotein in complex with the 67... -

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Basic information

Entry
Database: EMDB / ID: EMD-19017
TitleS1B domain of the PDCoV spike glycoprotein in complex with the 67B12 and 46E6 antibody Fab fragments
Map data
Sample
  • Complex: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
    • Protein or peptide: Spike protein
    • Protein or peptide: 67B12 antibody heavy chain
    • Protein or peptide: 67B12 antibody light chain
    • Protein or peptide: 46E6 antibody heavy chain
    • Protein or peptide: 46E6 antibody heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike / coronavirus / antibody / complex / RBD / S1B / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Porcine deltacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDebski-Antoniak O / Drulyte I / Hurdiss DL
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Innovative Medicines InitiativeLSHM19136 Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein.
Authors: Wenjuan Du / Oliver Debski-Antoniak / Dubravka Drabek / Rien van Haperen / Melissa van Dortmondt / Joline van der Lee / Ieva Drulyte / Frank J M van Kuppeveld / Frank Grosveld / Daniel L ...Authors: Wenjuan Du / Oliver Debski-Antoniak / Dubravka Drabek / Rien van Haperen / Melissa van Dortmondt / Joline van der Lee / Ieva Drulyte / Frank J M van Kuppeveld / Frank Grosveld / Daniel L Hurdiss / Berend-Jan Bosch /
Abstract: Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus ...Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
History
DepositionNov 30, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19017.png

Downloads & links

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Map

FileDownload / File: emd_19017.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291.999 Å		0.97 Å/pix.
x 300 pix.
= 291.999 Å		0.97 Å/pix.
x 300 pix.
= 291.999 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.30820972 - 0.634116
Average (Standard dev.)0.00039208593 (±0.012411781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19017_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_19017_half_map_1.map
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Histogram

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Half map: #1

Fileemd_19017_half_map_2.map
Projections & Slices
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Sample components

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Entire : PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibod...

EntireName: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
Components
  • Complex: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
    • Protein or peptide: Spike protein
    • Protein or peptide: 67B12 antibody heavy chain
    • Protein or peptide: 67B12 antibody light chain
    • Protein or peptide: 46E6 antibody heavy chain
    • Protein or peptide: 46E6 antibody heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibod...

SupramoleculeName: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.24 KDa

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine deltacoronavirus
Molecular weightTheoretical: 12.787479 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LEVVQLNISA HMDFGEARLD SVTINGNTSY CVTKPYFRLE TNFMCTGCTM NLRTDTCSFD LSAVNNGMSF SQFCLSTESG ACEMKIIVT YVWNYLLRQR LYVTAVEGQT HTGTT

UniProtKB: Spike protein

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Macromolecule #2: 67B12 antibody heavy chain

MacromoleculeName: 67B12 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.964826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVQSGAEV KKPGSSVKVS CKASGGTFSS LAISWVRQAP GQGLEWMGGI IPTFGTTNYA QNFRGRVTIT ADKSTSTAYM ELSTLISED TAVYFCARER STDTWPGDAF DIWGQGTMVT VSSASTKGPS VFPLAPSSGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
VQLVQSGAEV KKPGSSVKVS CKASGGTFSS LAISWVRQAP GQGLEWMGGI IPTFGTTNYA QNFRGRVTIT ADKSTSTAYM ELSTLISED TAVYFCARER STDTWPGDAF DIWGQGTMVT VSSASTKGPS VFPLAPSSGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLLGQTY ICNVNHKPSN TKVDKKVEPK

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Macromolecule #3: 67B12 antibody light chain

MacromoleculeName: 67B12 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.037592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EILMTQSPAT LSVSPGERAT LSCWASQSVN SKLAWYQQKP GQAPRLLIYD TSTRATGIPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNYWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EILMTQSPAT LSVSPGERAT LSCWASQSVN SKLAWYQQKP GQAPRLLIYD TSTRATGIPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNYWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS F

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Macromolecule #4: 46E6 antibody heavy chain

MacromoleculeName: 46E6 antibody heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.508619 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAMHWVRQA PGKGLEWVAV IWRDGSNEFY ADSVKGRFTI SRDNSKDTLY LQMNSLRAE DTAVYYCARR GIIMVRGLLG YWGQGTLVTV SSASTKGPSV FPLAPSSKSG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAMHWVRQA PGKGLEWVAV IWRDGSNEFY ADSVKGRFTI SRDNSKDTLY LQMNSLRAE DTAVYYCARR GIIMVRGLLG YWGQGTLVTV SSASTKGPSV FPLAPSSKSG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP K

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Macromolecule #5: 46E6 antibody heavy chain

MacromoleculeName: 46E6 antibody heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.017627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPPS LSASVGDRVT ITCRASQGIS NYLAWHQQKP GKVPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPPS LSASVGDRVT ITCRASQGIS NYLAWHQQKP GKVPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 245068
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bfu


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting was done using Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8r9z:
S1B domain of the PDCoV spike glycoprotein in complex with the 67B12 and 46E6 antibody Fab fragments

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