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

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Basic information

Entry
Database: PDB / ID: 9bnb
TitleCollagen XVIII trimerization domain with introduced inter-chain disulfide bond, G(-1)C-L5C
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
Collagen alpha-1(XVIII) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYoung, T. / Williams, J.C.
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


Theoretical massNumber of molelcules
Total (without water)19,6063
Polymers19,6063
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.475, 42.156, 84.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 6535.496 Da / Num. of mol.: 3 / Mutation: A(-1)C, L5C (authors' numbering)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris HCl, pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.5→37.72 Å / Num. obs: 24405 / % possible obs: 99.89 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1211 / Rpim(I) all: 0.03522 / Rrim(I) all: 0.1262 / Net I/σ(I): 11.67
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.9007 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2381 / CC1/2: 0.862 / CC star: 0.962 / Rpim(I) all: 0.2513 / Rrim(I) all: 0.9356 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→37.72 Å / SU ML: 0.1785 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 1180 4.84 %
Rwork0.2035 23210 -
obs0.205 24390 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 0 110 1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191366
X-RAY DIFFRACTIONf_angle_d1.25651862
X-RAY DIFFRACTIONf_chiral_restr0.0746203
X-RAY DIFFRACTIONf_plane_restr0.0169243
X-RAY DIFFRACTIONf_dihedral_angle_d15.2753505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.30131500.27342840X-RAY DIFFRACTION99.73
1.57-1.650.26321310.24042860X-RAY DIFFRACTION99.9
1.65-1.750.27921320.23232879X-RAY DIFFRACTION99.9
1.75-1.890.28231320.2412885X-RAY DIFFRACTION100
1.89-2.080.25821380.21262878X-RAY DIFFRACTION100
2.08-2.380.23871520.21342906X-RAY DIFFRACTION99.97
2.38-30.25721900.22282890X-RAY DIFFRACTION99.9
3-37.720.19791550.17683072X-RAY DIFFRACTION99.78

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