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- EMDB-19014: PDCoV spike glycoprotein ectodomain in complex with the 22C10 ant... -

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Basic information

Entry
Database: EMDB / ID: EMD-19014
TitlePDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment
Map data
Sample
  • Complex: PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment
    • Protein or peptide: Spike protein
    • Protein or peptide: 22C10 antibody heavy chain
    • Protein or peptide: 22C10 antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike / coronavirus / antibody / complex / PDCoV / VIRAL PROTEIN
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 / membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. ...Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Deltacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19014.png

Downloads & links

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Map

FileDownload / File: emd_19014.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 360 pix.
= 367.92 Å		1.02 Å/pix.
x 360 pix.
= 367.92 Å		1.02 Å/pix.
x 360 pix.
= 367.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.022 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.096
Minimum - Maximum-0.21536306 - 0.6310213
Average (Standard dev.)-0.0004859528 (±0.017408615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 367.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19014_msk_1.map
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Half map: #2

Fileemd_19014_half_map_1.map
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Half map: #1

Fileemd_19014_half_map_2.map
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Sample components

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Entire : PDCoV spike glycoprotein ectodomain in complex with the 22C10 ant...

EntireName: PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment
Components
  • Complex: PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment
    • Protein or peptide: Spike protein
    • Protein or peptide: 22C10 antibody heavy chain
    • Protein or peptide: 22C10 antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PDCoV spike glycoprotein ectodomain in complex with the 22C10 ant...

SupramoleculeName: PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 520 KDa

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Deltacoronavirus
Molecular weightTheoretical: 119.212852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DDLLDLLTFP GAHRFLHKPT RNSSSLYSRA NNNFDVGVLP GYPTKNVNLF SPLTNSTLPI NGLHRSYQPL MLNCLTKITN HTLSMYLLP SEIQTYSCGG AMVKYQTHDA VRIILDLTAT DHISVEVVGQ HGENYVFVCS EQFNYTTALH NSTFFSLNSE L YCFTNNTY ...String:
DDLLDLLTFP GAHRFLHKPT RNSSSLYSRA NNNFDVGVLP GYPTKNVNLF SPLTNSTLPI NGLHRSYQPL MLNCLTKITN HTLSMYLLP SEIQTYSCGG AMVKYQTHDA VRIILDLTAT DHISVEVVGQ HGENYVFVCS EQFNYTTALH NSTFFSLNSE L YCFTNNTY LGILPPDLTD FTVYRTGQFY ANGYLLGTLP ITVNYVRLYR GHLSANSAHF ALANLTDTLI TLTNTTISQI TY CDKSVVD SIACQRSSHE VEDGFYSDPK SAVRARQRTI VTLPKLPELE VVQLNISAHM DFGEARLDSV TINGNTSYCV TKP YFRLET NFMCTGCTMN LRTDTCSFDL SAVNNGMSFS QFCLSTESGA CEMKIIVTYV WNYLLRQRLY VTAVEGQTHT GTTS VHATD TSSVITDVCT DYTIYGVSGT GIIKPSDLLL HNGIAFTSPT GELYAFKNIT TGKTLQVLPC ETPSQLIVIN NTVVG AITS SNSTENNRFT TTIVTPTFFY STNATTFNCT KPVLSYGPIS VCSDGAIVGT STLQNTRPSI VSLYDGEVEI PSAFSL SVQ TEYLQVQAEQ VIVDCPQYVC NGNSRCLQLL AQYTSACSNI EAALHSSAQL DSREIINMFQ TSTQSLQLAN ITNFKGD YN FSSILTTRIG GRSAIEDLLF NKVVTSGLGT VDQDYKSCSR DMAIADLVCS QYYNGIMVLP GVVDAEKMAM YTGSLTGA M VFGGLTAAAA IPFATAVQAR LNYVALQTNV LQENQKILAE SFNQAVGNIS LALSSVNDAI QQTSEALNTV AIAIKKIQT VVNQQGEALS HLTAQLSNNF QAISTSIQDI YNRLEEVEAN QQVDRLITGR LAALNAYVTQ LLNQMSQIRQ SRLLAQQKIN ECVKSQSPR YGFCGNGTHI FSLTQTAPNG IFFMHAVLVP NKFTRVNASA GICVDNTRGY SLQPQLILYQ FNNSWRVTPR N MYEPRLPR QADFIQLTDC SVTFYNTTAA NLPNIIPDII DVNQTVSDII DNLPTATPPQ WDVGIYNNTI LNLTVEINDL QE RSKNLSQ IADRLQNYID NLNNTLVDLE WLNRVETYLK WP

UniProtKB: Spike protein

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Macromolecule #2: 22C10 antibody heavy chain

MacromoleculeName: 22C10 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.107698 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVRLLESGGG LVQPGGSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVSI ITDSGGGTYF ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTALYYCVKV GFCYSSTCPF DYWGQGTLVT VS

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Macromolecule #3: 22C10 antibody light chain

MacromoleculeName: 22C10 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.553769 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ELVMTQSPAT LSVSPGERAT LSCRASQSVS SDLAWYQQRP GRAPRLLIYD ASTRTTGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCH QYNNWLTFGQ GTRLEI

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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: 33 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168789
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 model
PDB IDChain

6bfu

chain_id: A, source_name: PDB, initial_model_type: experimental model

6bfu

chain_id: B, source_name: PDB, initial_model_type: experimental model

6bfu

chain_id: C, source_name: PDB, 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-8r9w:
PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment

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