9C7Z | pdb_00009c7z

Hallucinated C3 protein assembly HALC3_919


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9C7Z

This is version 1.1 of the entry. See complete history

Literature

Designed miniproteins potently inhibit and protect against MERS-CoV.

Ragotte, R.J.Tortorici, M.A.Catanzaro, N.J.Addetia, A.Coventry, B.Froggatt, H.M.Lee, J.Stewart, C.Brown, J.T.Goreshnik, I.Sims, J.N.Milles, L.F.Wicky, B.I.M.Glogl, M.Gerben, S.Kang, A.Bera, A.K.Sharkey, W.Schafer, A.Harkema, J.R.Baric, R.S.Baker, D.Veesler, D.

(2025) Cell Rep 44: 115760-115760

  • DOI: https://doi.org/10.1016/j.celrep.2025.115760
  • Primary Citation Related Structures: 
    9C7Z, 9DGO, 9DKK

  • PubMed Abstract: 

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen with a 36% case-fatality rate in humans. No vaccines or specific therapeutics are currently approved for use in humans or the camel host reservoir. Here, we computationally designed monomeric and homo-oligomeric miniproteins that bind with high affinity to the MERS-CoV spike (S) glycoprotein, the main target of neutralizing antibodies and vaccine development. We show that these miniproteins broadly neutralize a panel of MERS-CoV S variants, spanning the known antigenic diversity of this pathogen, by targeting a conserved site in the receptor-binding domain (RBD). The miniproteins directly compete with binding of the dipeptidylpeptidase 4 (DPP4) receptor to MERS-CoV S, thereby blocking viral attachment to the host entry receptor and subsequent membrane fusion. Intranasal administration of a lead miniprotein provides prophylactic protection against stringent MERS-CoV challenge in mice, motivating its future clinical development as a next-generation countermeasure against this virus with pandemic potential.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 16.35 kDa 
  • Atom Count: 1,018 
  • Modeled Residue Count: 131 
  • Deposited Residue Count: 138 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HALC3_919
A, B
69synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.373α = 90
b = 78.373β = 90
c = 78.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references