Skip to main content

 9PI7 | pdb_00009pi7

EV-D68 in complex with G12 VHH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9PI7

This is version 1.1 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 34: 4136-4152

  • DOI: https://doi.org/10.1016/j.ymthe.2026.04.021
  • Primary Citation Related Structures: 
    9PI7, 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: 109.28 kDa 
  • Atom Count: 7,187 
  • Modeled Residue Count: 926 
  • Deposited Residue Count: 995 
  • 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
G12 VHH123Vicugna pacosMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



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: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references