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- EMDB-44725: SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric ant... -

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Basic information

Entry
Database: EMDB / ID: EMD-44725
TitleSARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist
Map data
Sample
  • Complex: Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonist
    • Complex: Trimeric T3A antagonist
      • Protein or peptide: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 spike HexaPro protein trimer
      • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordstrimeric 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 / symbiont-mediated disruption of host tissue / endopeptidase activity / 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 / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsYoung T
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44725.png

Downloads & links

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Map

FileDownload / File: emd_44725.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0982994 - 0.2880127
Average (Standard dev.)0.001151857 (±0.01236423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44725_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44725_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A ant...

EntireName: Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonist
Components
  • Complex: Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonist
    • Complex: Trimeric T3A antagonist
      • Protein or peptide: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 spike HexaPro protein trimer
      • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A ant...

SupramoleculeName: Complex of SARS-CoV-2 spike HexaPro protein with trimeric T3A antagonist
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Purified spike protein and T3A antagonist complex isolated by size exclusion chromatography.

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Supramolecule #2: Trimeric T3A antagonist

SupramoleculeName: Trimeric T3A antagonist / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Collagen XVIII trimerization domain with extracellular ACE2 domain (3 residue linker), trimer
Source (natural)Organism: Homo sapiens (human) / Location in cell: Transmembrane

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Supramolecule #3: SARS-CoV-2 spike HexaPro protein trimer

SupramoleculeName: SARS-CoV-2 spike HexaPro protein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Stabilized SARS-CoV-2 spike protein, trimer
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting en...

MacromoleculeName: Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2
type: protein_or_peptide / ID: 1
Details: residues 1442-1496 (Uniprot numbering) of collagen chain, followed by a linker and then residues 19-614 of ACE2
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.565625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSLILLFL VAVATRVLSH HHHHHGSSGV RLWATRQAML GQVHEVPEGW LIFVAEQEEL YVRVQNGFRK VQLEARTPLP RGSGSTIEE QAKTFLDKFN HEAEDLFYQS SLASWNYNTN ITEENVQNMN NAGDKWSAFL KEQSTLAQMY PLQEIQNLTV K LQLQALQQ ...String:
MGWSLILLFL VAVATRVLSH HHHHHGSSGV RLWATRQAML GQVHEVPEGW LIFVAEQEEL YVRVQNGFRK VQLEARTPLP RGSGSTIEE QAKTFLDKFN HEAEDLFYQS SLASWNYNTN ITEENVQNMN NAGDKWSAFL KEQSTLAQMY PLQEIQNLTV K LQLQALQQ NGSSVLSEDK SKRLNTILNT MSTIYSTGKV CNPDNPQECL LLEPGLNEIM ANSLDYNERL WAWESWRSEV GK QLRPLYE EYVVLKNEMA RANHYEDYGD YWRGDYEVNG VDGYDYSRGQ LIEDVEHTFE EIKPLYEHLH AYVRAKLMNA YPS YISPIG CLPAHLLGDM WGRFWTNLYS LTVPFGQKPN IDVTDAMVDQ AWDAQRIFKE AEKFFVSVGL PNMTQGFWEN SMLT DPGNV QKAVCHPTAW DLGKGDFRIL MCTKVTMDDF LTAHHEMGHI QYDMAYAAQP FLLRNGANEG FHEAVGEIMS LSAAT PKHL KSIGLLSPDF QEDNETEINF LLKQALTIVG TLPFTYMLEK WRWMVFKGEI PKDQWMKKWW EMKREIVGVV EPVPHD ETY CDPASLFHVS NDYSFIRYYT RTLYQFQFQE ALCQAAKHEG PLHKCDISNS TEAGQKLFNM LRLGKSEPWT LALENVV GA KNMNVRPLLN YFEPLFTWLK DQNKNSFVGW STDWSPYA

UniProtKB: Collagen alpha-1(XVIII) chain, Angiotensin-converting enzyme 2

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 142.427438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSA WSHP QFEK

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration0.33 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.137 MNaClsodium chloride
0.0027 MKClpotassium chloride
0.01 MNa2HPO4sodium phosophate dibasic
0.0018 MKH2PO4potassium phosphate monobasic

Details: 1x PBS 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5234 / Average exposure time: 2.157 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1616068 / Details: Automated Blob Picker Diameter 150 - 300
CTF correctionSoftware - Name: cryoSPARC
Details: Patch motion correction and Patch CTF applied after Import Movies and before Blob Picker
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 225636
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 113000 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

6m0j

source_name: PDB, initial_model_type: experimental model

6vxx

source_name: PDB, initial_model_type: experimental model
DetailsInitial 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)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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