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- EMDB-76232: Structure of the Porcine deltacoronavirus (PDCoV) receptor-bindin... -

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Basic information

Entry
Database: EMDB / ID: EMD-76232
TitleStructure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody (local refinement)
Map dataUnsharpened map
Sample
  • Complex: Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa light chain nanobody
    • Protein or peptide: PDCoV IL121_2014 receptor binding domain
    • Protein or peptide: RBD minibinder 11
  • Ligand: water
Keywordsporcine deltacoronavirus / minibinder / protein design / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Function / homology
Function and homology information


negative regulation of collateral sprouting / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / negative regulation of axon regeneration / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane ...negative regulation of collateral sprouting / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / negative regulation of axon regeneration / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / heparin binding / synaptic vesicle membrane / growth cone / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / perikaryon / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / axon / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
: / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain ...: / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S / Spike protein
Similarity search - Component
Biological speciesPorcine deltacoronavirus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsAvery NG / Park YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Computational design of an ultrapotent deltacoronavirus miniprotein inhibitor.
Authors: Nathan G Avery / Courtney N Yoshiyama / Ashley L Taylor / Young-Jun Park / Daniel Asarnow / Lisa Perruzza / Jack T Brown / Davide Corti / Fabio Benigni / Tyler N Starr / David Veesler /
Abstract: Multiple spillovers of porcine deltacoronavirus (PDCoV) into humans in Haiti highlight its zoonotic potential and the need for targeted interventions. No approved vaccines or therapeutics are ...Multiple spillovers of porcine deltacoronavirus (PDCoV) into humans in Haiti highlight its zoonotic potential and the need for targeted interventions. No approved vaccines or therapeutics are available for use in humans against any DCoVs. Here, we report the de novo design of PDCoV miniprotein inhibitors (aka minibinders, MBs) and show that one of them, MB11, binds with picomolar affinity to the PDCoV receptor-binding domain (RBD). MB11 potently inhibits PDCoV, outcompeting monoclonal antibodies, and cross-reacts with and broadly neutralizes a panel of distantly related DCoVs. We determined a cryoelectron microscopy structure of MB11 bound to the PDCoV RBD which reveals the molecular basis of broad DCoV neutralization through interference with host receptor engagement. Deep mutational scanning of the PDCoV RBD reveals that MB11 has a high barrier to viral escape with only few mutations mediating escape without dampening APN receptor binding. MB11 resists stringent biochemical stresses, including high temperature, low pH, and proteolysis, which may enable delivery to various tissues for viral inhibition. This work delineates a prime candidate for clinical evaluation against PDCoV infection and for pandemic preparedness.
History
DepositionMar 21, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76232.png

Downloads & links

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Map

FileDownload / File: emd_76232.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 288 pix.
= 288.864 Å		1 Å/pix.
x 288 pix.
= 288.864 Å		1 Å/pix.
x 288 pix.
= 288.864 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5037342 - 1.3652405
Average (Standard dev.)0.00041935898 (±0.017615924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 288.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76232_msk_1.map
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Mask #2

Fileemd_76232_msk_2.map
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Additional map: Sharpened map by b-factor -117

Fileemd_76232_additional_1.map
AnnotationSharpened map by b-factor -117
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Half map: Half map A

Fileemd_76232_half_map_1.map
AnnotationHalf map A
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Histogram

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Half map: Half map B

Fileemd_76232_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa ...

EntireName: Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa light chain nanobody
Components
  • Complex: Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa light chain nanobody
    • Protein or peptide: PDCoV IL121_2014 receptor binding domain
    • Protein or peptide: RBD minibinder 11
  • Ligand: water

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Supramolecule #1: Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa ...

SupramoleculeName: Complex of PDCoV RBD, RBD minibinder 11, PD3 Fab, and anti-kappa light chain nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Porcine deltacoronavirus

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Macromolecule #1: PDCoV IL121_2014 receptor binding domain

MacromoleculeName: PDCoV IL121_2014 receptor binding domain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase
Source (natural)Organism: Porcine deltacoronavirus
Molecular weightTheoretical: 19.2859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTPELEVVQL NISAHMDFGE ARLDSVTING NTSYCVTKPY FRLETNFMCT GCTMNLRTD TCSFDLSAVN NGMSFSQFCL STESGACEMK IIVTYVWNYL LRQRLYVTAV EGQTHTGGGS GLNDIFEAQK I EWHEGGSH HHHHHHH

UniProtKB: Receptor-type tyrosine-protein phosphatase S, Spike protein

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Macromolecule #2: RBD minibinder 11

MacromoleculeName: RBD minibinder 11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.905779 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHHHG GSLVPRGSGG SGLNDIFEAQ KIEWHEGGSH MLTREEVQAI IDGHVIEVKY DSVEEFLEKY KGKISEETIE LIEKLIELT SKDPKLSRLP LIFMQMLDMF IEIMKDLKDR GITSEEDRKL LYDVFKERFE QWFDSFWPGE EEIKEIMLKI L DLLYNEDY EKIYEAEK

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 46 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: Leginon
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10236 / Average exposure time: 5.0 sec. / Average electron dose: 52.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 512440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-11zv:
Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody (local refinement)

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