9PI8 | pdb_00009pi8

EV-D68 in complex with G12 Fc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

An RNA-to-RNA pipeline for rapid antiviral antibody development.

Hodge, E.A.Archer, J.Anderson, J.S.Warner, N.L.Tremblay, J.Klose, T.Park, S.Hinkley, T.Khandhar, A.P.Kuhn, R.Shoemaker, C.B.Erasmus, J.H.

(2026) Mol Ther 

  • DOI: https://doi.org/10.1016/j.ymthe.2026.04.021
  • Primary Citation Related Structures: 
    9PI8

  • PubMed Abstract: 

    Rapid development of antibody therapeutics is often hindered by dependencies on recombinant protein production, both for antigen generation and for antibody manufacturing. To overcome these bottlenecks, we established a self-amplifying replicon RNA (repRNA) immunization and therapeutic delivery platform that enables an end-to-end RNA-to-antibody-to-RNA workflow. In this approach, alpacas are immunized with repRNA encoding virus-like particles to elicit antibody responses, peripheral blood mononuclear cells are harvested to construct phage display libraries, and broadly neutralizing heavy-chain-only antibodies (VHHs [variable heavy domain of the heavy chain]) are identified through high-throughput screening. Lead VHHs are then re-encoded into repRNA for in vivo delivery as therapeutic constructs, with engineering options for valency, potency, and serum half-life. As proof of concept, we applied this platform against enterovirus D68 (EV-D68), an emerging pathogen associated with severe respiratory disease and acute flaccid myelitis in children for which no vaccines or treatments exist. repRNA-encoded VHHs protected mice from EV-D68 challenge in both lungs and nasal cavities, and cryoelectron microscopy revealed the capsid-binding footprint and mechanism of neutralization. Together, these findings demonstrate a modular platform for rapid discovery and delivery of antiviral biologics, with EV-D68 serving as a prototype application.


  • Organizational Affiliation
    • HDT Bio, Seattle, WA 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 136.76 kDa 
  • Atom Count: 7,187 
  • Modeled Residue Count: 926 
  • Deposited Residue Count: 1,239 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
viral protein 1309enterovirus D68Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
viral protein 2248enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A0A7X639 (Human enterovirus D68)
Explore A0A0A7X639 
Go to UniProtKB:  A0A0A7X639
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7X639
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
viral protein 3247enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
viral protein 468enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
G12 Fc fusion367Vicugna pacosMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN75N9302200035

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release