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- EMDB-46804: PDCoV S trimer bound by three copies of PD41 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-46804
TitlePDCoV S trimer bound by three copies of PD41 Fab
Map dataPDCoV-S trimer bound by three copies of PD41 Fab, raw map
Sample
  • Complex: Complex of PDCoV S trimer with PD41 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: PD41 Fab variable heavy-chain
    • Protein or peptide: PD41 Fab variable light-chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID
Keywordscoronavirus / spike / antibody / PDCoV / PD41 / complex / VIRAL PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 superfamily, coronavirus / 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. ...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 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesDeltacoronavirus PDCoV/USA/Illinois121/2014 / Porcine deltacoronavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsAsarnow D / Rexhepaj M / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI167966 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP1AI158186 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD032290 United States
Burroughs Wellcome Fund United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Immunity / Year: 2024
Title: Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.
Authors: Megi Rexhepaj / Daniel Asarnow / Lisa Perruzza / Young-Jun Park / Barbara Guarino / Mathew Mccallum / Katja Culap / Christian Saliba / Giada Leoni / Alessio Balmelli / Courtney N Yoshiyama / ...Authors: Megi Rexhepaj / Daniel Asarnow / Lisa Perruzza / Young-Jun Park / Barbara Guarino / Mathew Mccallum / Katja Culap / Christian Saliba / Giada Leoni / Alessio Balmelli / Courtney N Yoshiyama / Miles S Dickinson / Joel Quispe / Jack T Brown / M Alejandra Tortorici / Kaitlin R Sprouse / Ashley L Taylor / Davide Corti / Tyler N Starr / Fabio Benigni / David Veesler /
Abstract: Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are ...Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.
History
DepositionAug 29, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46804.png

Downloads & links

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Map

FileDownload / File: emd_46804.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPDCoV-S trimer bound by three copies of PD41 Fab, raw map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 432 pix.
= 360.72 Å		0.84 Å/pix.
x 432 pix.
= 360.72 Å		0.84 Å/pix.
x 432 pix.
= 360.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.07561583 - 0.17768805
Average (Standard dev.)0.00012144259 (±0.005367858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 360.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46804_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_46804_msk_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: PDCoV-S trimer bound by three copies of PD41 Fab, sharpened map

Fileemd_46804_additional_1.map
AnnotationPDCoV-S trimer bound by three copies of PD41 Fab, sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PDCoV-S trimer bound by three copies of PD41 Fab, half map A

Fileemd_46804_half_map_1.map
AnnotationPDCoV-S trimer bound by three copies of PD41 Fab, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PDCoV-S trimer bound by three copies of PD41 Fab, half map B

Fileemd_46804_half_map_2.map
AnnotationPDCoV-S trimer bound by three copies of PD41 Fab, half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of PDCoV S trimer with PD41 Fab

EntireName: Complex of PDCoV S trimer with PD41 Fab
Components
  • Complex: Complex of PDCoV S trimer with PD41 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: PD41 Fab variable heavy-chain
    • Protein or peptide: PD41 Fab variable light-chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITOLEIC ACID

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Supramolecule #1: Complex of PDCoV S trimer with PD41 Fab

SupramoleculeName: Complex of PDCoV S trimer with PD41 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Deltacoronavirus PDCoV/USA/Illinois121/2014
Molecular weightTheoretical: 530 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 deltacoronavirus
Molecular weightTheoretical: 128.934805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQRALLIMTL LCLVRAKFAD DLLDLLTFPG AHRFLHKLTS NSSSLYSRAN NFDVGVLPGY PTKNVNLFSP LTNSTLPING LHRSYQPLM LNCLTKITNH TLSMYLLPSE IQTYSCGGAM VKYQTHDAVR IILDLTVTDH ISVEVVGQHG ENYVFVCSEQ F NYTTALHN ...String:
MQRALLIMTL LCLVRAKFAD DLLDLLTFPG AHRFLHKLTS NSSSLYSRAN NFDVGVLPGY PTKNVNLFSP LTNSTLPING LHRSYQPLM LNCLTKITNH TLSMYLLPSE IQTYSCGGAM VKYQTHDAVR IILDLTVTDH ISVEVVGQHG ENYVFVCSEQ F NYTTALHN STFFSLNSEL YCFTNNTYLG ILPPDLTDFT VYRTGQFYAN GYLLGTLPIT VNYVRLYRGH LSANSAHFAL AN LTDTLIT LTNTTISQIT YCDKSVVDSI ACQRSSHEVE DGFYSDPKSA VRARQRTIVT LPKLPELEVV QLNISAHMDF GEA RLDSVT INGNTSYCVT KPYFRLETNF MCTGCTINLR TDTCSFDLSA VNNGMSFSQF CLSTESGACE MKIVVTYVWK YLLR QRLYV TAVEGQTHTG TTSVHAIDTS SVITDVCTDY TIYGVSGTGI IKPSDLLLHN GIAFTSPTGE LYAFKNITTG KTLQV LPCE TPSQLIVINN TVVGAITSSN STENNRFTTT IVTPTFFYST NATTFNCTKP VLSYGPISVC SDGAIVGTST LQNTRP SIV SLYDGEVEIP SAFSLSVQTE YLQVQAEQVI VDCPQYVCNG NSRCLQLLAQ YTSACSNIEA ALHSSAQLDS REIINMF QT STQSLQLANI TNFKGDYNFS SILTTRLGGR SAIEDLLFNK VVTSGLGTVD QDYKACSRDM AIADLVCSQY YNGIMVLP G VVDAEKMAMY TGSLTGAMVF GGLTAAAAIP FATAVQARLN YVALQTNVLQ ENQKILAESF NQAVGNISLA LSSVNDAIQ QTSEALNTVA IAIKKIQTVV NQQGEALSHL TAQLSNNFQA ISTSIQDIYN RLEEVEANQQ VDRLITGRLA ALNAYVTQLL NQMSQIRQS RLLAQQKINE CVKSQSSRYG FCGNGTHIFS LTQTAPNGIF FMHAVLVPNK FTRVNASAGI CVDNTRGYSL Q PQLILYQF NNSWRVTPRN MYEPRLPRQA DFIQLTDCSV TFYNTTAANL PNIIPDIIDV NQTVSDIIDN LPTATPPQWD VG IYNNTIL NLTVEINDLQ ERSKNLSQIA DRLQNYIDNL NNTLVDLEWL NRVETYLKWP GSGYIPEAPR DGQAYVRKDG EWV LLSTFL GRSLEVLFQG PGSGGLNDIF EAQKIEWHEG SGHHHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: PD41 Fab variable heavy-chain

MacromoleculeName: PD41 Fab variable heavy-chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: ATX
Molecular weightTheoretical: 13.02051 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
HSQLQESGPG LVKPSQTLSL TCTVSGGSIS SAGYYWNWIR QHPGKGLEWI GYIYYSGNTY YNPSLKSRVT ISVDTSKSQF SLKLNSVTA ADTAVYYCAR KIVNWFDPWG QGTLVTVSS

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Macromolecule #3: PD41 Fab variable light-chain

MacromoleculeName: PD41 Fab variable light-chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: ATX
Molecular weightTheoretical: 11.61767 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTSSDVG GYNYVSWYQQ HPGKAPKLMI YDVSERPSGV SNRFSGSKSG NTASLTISGL QAEDEADYF CCSYAAYTTY VVFGGGTQLT VL

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 7 / Number of copies: 3 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
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

BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time 6 seconds, force -1.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 19556 / Average exposure time: 4.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5732849
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 26247
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software: (Name: RELION, cryoSPARC)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6bfu

chain_id: A, source_name: PDB, initial_model_type: experimental model
chain_id: I, source_name: Other, initial_model_type: in silico modelABodyBuilder2
chain_id: M, source_name: Other, initial_model_type: in silico modelABodyBuilder2
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9dez:
PDCoV S trimer bound by three copies of PD41 Fab

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