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- PDB-9bnc: Collagen XVIII trimerization domain with introduced inter-chain d... -

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Basic information

Entry
Database: PDB / ID: 9bnc
TitleCollagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C
ComponentsCollagen alpha-1(XVIII) chain
KeywordsSTRUCTURAL PROTEIN / Trimer / Disulfide / Biologic scaffold
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 / Collagen degradation ...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 / Collagen degradation / basement membrane / Integrin cell surface interactions / visual perception / animal organ morphogenesis / skeletal system development / : / angiogenesis / cell adhesion / endoplasmic reticulum lumen / response to xenobiotic stimulus / negative regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / metal ion binding
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 / C-type lectin fold / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Collagen alpha-1(XVIII) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
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

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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
B: Collagen alpha-1(XVIII) chain
C: Collagen alpha-1(XVIII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6355
Polymers19,4323
Non-polymers2022
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-34 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.360, 58.078, 67.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Collagen alpha-1(XVIII) chain


Mass: 6477.461 Da / Num. of mol.: 3 / Fragment: trimerization domain / Mutation: E31C, V37C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL18A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39060
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1 M Tris HCl, pH 8.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.4→32.01 Å / Num. obs: 29542 / % possible obs: 97.39 % / Redundancy: 11.5 % / Biso Wilson estimate: 13.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05122 / Rpim(I) all: 0.01488 / Rrim(I) all: 0.05341 / Net I/σ(I): 26.71
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.215 / Num. unique obs: 2435 / CC1/2: 0.956 / CC star: 0.989 / Rpim(I) all: 0.1018 / Rrim(I) all: 0.2396 / % possible all: 81.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→32.01 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 1427 4.83 %
Rwork0.171 --
obs0.1722 29539 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 12 175 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.094
X-RAY DIFFRACTIONf_dihedral_angle_d8.02213
X-RAY DIFFRACTIONf_chiral_restr0.088207
X-RAY DIFFRACTIONf_plane_restr0.014251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.23931260.19342309X-RAY DIFFRACTION81
1.45-1.510.22241340.18512613X-RAY DIFFRACTION93
1.51-1.580.19341430.17912853X-RAY DIFFRACTION100
1.58-1.660.24721560.17732836X-RAY DIFFRACTION100
1.66-1.760.20751460.17462864X-RAY DIFFRACTION100
1.76-1.90.20611500.17772848X-RAY DIFFRACTION100
1.9-2.090.18821340.16372895X-RAY DIFFRACTION100
2.09-2.390.17371440.15772896X-RAY DIFFRACTION100
2.39-3.020.21141310.18082949X-RAY DIFFRACTION100
3.02-32.010.18361630.16633049X-RAY DIFFRACTION100

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