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- PDB-9bne: SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric ant... -

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Basic information

Entry
Database: PDB / ID: 9bne
TitleSARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist
Components
  • Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/ANTAGONIST / trimeric antagonist SARS-CoV-2 complex / PROTEIN BINDING / VIRAL PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / Laminin interactions / collagen trimer / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / positive regulation of amino acid transport ...response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / Laminin interactions / collagen trimer / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / Collagen degradation / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / basement membrane / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / Integrin cell surface interactions / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / viral life cycle / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / visual perception / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / animal organ morphogenesis / skeletal system development / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / : / virus receptor activity / regulation of inflammatory response / angiogenesis / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / cell adhesion / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / response to xenobiotic stimulus / negative regulation of cell population proliferation / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / : ...Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / : / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin-like/link domain superfamily / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / C-type lectin fold / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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
Spike glycoprotein / Collagen alpha-1(XVIII) chain / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsYoung, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Commun Biol / Year: 2025
Title: Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist.
Authors: Juliet Gonzales / Tynan Young / Hyeran Choi / Miso Park / Yead Jewel / Chengcheng Fan / Rahul Purohit / Pamela J Bjorkman / John C Williams /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.
History
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
B: Spike glycoprotein
C: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
D: Spike glycoprotein
E: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)675,37251
Polymers662,9796
Non-polymers12,39345
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, KD < 1 nM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2


Mass: 78565.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: residues 1442-1496 (Uniprot numbering) of collagen chain, followed by a linker and then residues 19-614 of ACE2
Source: (gene. exp.) Homo sapiens (human) / Gene: COL18A1, ACE2, UNQ868/PRO1885 / Cell line (production host): HEK293, Expi293 / Production host: Homo sapiens (human) / Variant (production host): Expi293 / References: UniProt: P39060, UniProt: Q9BYF1
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 142427.438 Da / Num. of mol.: 3 / Fragment: extracellular portion
Mutation: hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): Expi293 / References: UniProt: P0DTC2
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 33
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonistCOMPLEXPurified spike protein and T3A antagonist complex isolated by size exclusion chromatography.#1-#20MULTIPLE SOURCES
2Trimeric T3A antagonistCOMPLEXCollagen XVIII trimerization domain with extracellular ACE2 domain (3 residue linker), trimer#11RECOMBINANT
3SARS-CoV-2 spike HexaPro protein trimerCOMPLEXStabilized SARS-CoV-2 spike protein, trimer#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular location
32Homo sapiens (human)9606Transmembrane
43Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
32Homo sapiens (human)9606Expi293Embryonic Kidney
43Homo sapiens (human)9606Expi293Embryonic KidneypalphaH
Buffer solutionpH: 7.4
Details: 1x PBS 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
Buffer component
IDConc.NameFormulaBuffer-ID
10.137 Msodium chlorideNaCl1
20.0027 Mpotassium chlorideKCl1
30.01 Msodium phosophate dibasicNa2HPO41
40.0018 Mpotassium phosphate monobasicKH2PO41
SpecimenConc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2.157 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5234

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7PyMOLmodel fitting
8Cootmodel fitting
9PHENIXmodel fitting
11Cootmodel refinement
12PHENIXmodel refinement
13cryoSPARCinitial Euler assignment
14cryoSPARCfinal Euler assignment
15cryoSPARCclassification
16cryoSPARC3D reconstruction
CTF correctionDetails: Patch motion correction and Patch CTF applied after Import Movies and before Blob Picker
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1616068 / Details: Automated Blob Picker Diameter 150 - 300
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225636 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting done by superposition of three components of 6M0J (complex of ACE2 and RBD of SARS-CoV-2 spike protein) onto each of the three RBDs of 6VXX (full SARS-CoV-2 spike hexapro protein trimer)
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16M0J

6m0j

16M0J1PDBexperimental model
26VXX

6vxx

16VXX2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00441043
ELECTRON MICROSCOPYf_angle_d0.4955825
ELECTRON MICROSCOPYf_dihedral_angle_d13.56714799
ELECTRON MICROSCOPYf_chiral_restr0.0426328
ELECTRON MICROSCOPYf_plane_restr0.0037152

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