9Y7F | pdb_00009y7f

Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel Nav1.7 P-loop 1.

• PDB DOI: https://doi.org/10.2210/pdb9Y7F/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Vicugna pacos, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-09-10 Released: 2026-09-16 
• Deposition Author(s): Chen, K.-E., Liu, J., Mobli, M., Collins, B.M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: in silico

Literature

Antigen-Detected NMR for Minimal Epitope Engineering and Structure-Guided Selection of a Na V 1.7-Selective Nanobody.

Liu, J., Chen, W., Cristofori-Armstrong, B., Crawford, T., Chen, K.E., Xie, P., Chan, R.W.B., Zhu, Y., Golder, M., Pereira Schmidt, A., Naughton, J.D., Condon, N.D., Andersson, A., Dehkhoda, F., McMahon, K.L., Klasfauseweh, T., Thapa, A., Tran, H., Tran, P., Jami, S., Ragnarsson, L., Furness, S.G.B., Deuis, J.R., Collins, B.M., Tham, W.H., Prasadam, I., Vetter, I., Mobli, M.

(2026) Adv Sci (Weinh) : e77611-e77611

• PubMed: 42702812 
• DOI: https://doi.org/10.1002/advs.77611
• Primary Citation Related Structures: 
  9Y7F


• PubMed Abstract: 
  

  Selective molecular recognition of membrane proteins is challenging because they contain few solvent-exposed extracellular epitopes, which often depend on their native environment for structure, making them difficult to isolate faithfully for binder discovery. Here, we show that antigen-detected NMR is well suited both to characterizing the folding of engineered minimal epitopes from the human voltage-gated sodium channel Na _V 1.7 and to selecting binders that recognize their solvent-exposed surfaces. Isotope labelling of the antigen enables NMR resonance assignment to assess retained local secondary structure, while ¹⁵ N titration and zz-exchange mapping provide binding and interface information. Combined with AlphaFold2 complex prediction, this creates a practical method for screening and ranking candidate binders. The approach was further validated by a high-resolution x-ray structure of an antigen-nanobody complex. Applying this workflow identified R4C8, a subtype- and species-selective nanobody whose binding to the extracellular surface of human Na _V 1.7 is supported by zz-exchange mapping, modelling, and cellular recognition, and which has minimal effects on channel gating. R4C8 detected Na _V 1.7 in engineered cell lines and in primary osteoarthritis-derived chondrocytes, providing a useful tool for selective target detection. These results show how antigen-detected NMR can support peptide engineering and structure-guided protein binder selection against minimal epitopes.

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Organizational Affiliation: 
• Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia.
Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.
Centre for Biomedical Technologies, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland, Australia.
School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, Queensland, Australia.
The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia.
Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia.
Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.
Research School of Biology, The Australian National University, Canberra, Australia.
School of Pharmacy and Pharmaceutical Sciences, The University of Queensland, Woolloongabba, Queensland, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.88 kDa 
• Atom Count: 1,287 
• Modeled Residue Count: 151 
• Deposited Residue Count: 158 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody R3D8	A	127	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 9 subunit alpha	B	31	Homo sapiens	Mutation(s): 2  Gene Names: SCN9A, NENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens) Explore Q15858  Go to UniProtKB:  Q15858
PHAROS:  Q15858 GTEx:  ENSG00000169432

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.829	α = 90
b = 43.636	β = 107.84
c = 42.325	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Chen, K.-E., Liu, J., Mobli, M., Collins, B.M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1156493
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1136021

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release