9BNB | pdb_00009bnb

Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, G(-1)C-L5C

• PDB DOI: https://doi.org/10.2210/pdb9BNB/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-02 Released: 2025-08-27 
• Deposition Author(s): Young, T., Williams, J.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist.

Gonzales, J., Young, T., Choi, H., Park, M., Jewel, Y., Fan, C., Purohit, R., Bjorkman, P.J., Williams, J.C.

(2025) Commun Biol 8: 1428-1428

• PubMed: 41053501 
• DOI: https://doi.org/10.1038/s42003-025-08819-w
• Primary Citation Related Structures: 
  9BNB, 9BNC, 9BND, 9BNE, 9BNF, 9BNG


• PubMed 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. 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.

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Organizational Affiliation: 
• Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.
Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA. [e-mail].
Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.61 kDa 
• Atom Count: 1,441 
• Modeled Residue Count: 167 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(XVIII) chain	A, B, C	57	Homo sapiens	Mutation(s): 2  Gene Names: COL18A1
UniProt & NIH Common Fund Data Resources
Find proteins for P39060 (Homo sapiens) Explore P39060  Go to UniProtKB:  P39060
PHAROS:  P39060 GTEx:  ENSG00000182871

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.475	α = 90
b = 42.156	β = 90
c = 84.464	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Young, T., Williams, J.C.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2025-10-29
  Changes: Database references