8YHZ | pdb_00008yhz

The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YHZ

This is version 1.2 of the entry. See complete history

Literature

Intra-channel bi-epitopic crosslinking unleashes ultrapotent antibodies targeting Na V 1.7 for pain alleviation.

Zhang, Y.Ding, Y.Zeng, Z.Zhu, R.Zheng, P.Fan, S.Cao, Q.Chen, H.Ren, W.Wu, M.Wang, L.Du, J.

(2024) Cell Rep Med 5: 101800-101800

  • DOI: https://doi.org/10.1016/j.xcrm.2024.101800
  • Primary Citation Related Structures: 
    8YHZ

  • PubMed Abstract: 

    Crucial for cell activities, ion channels are key drug discovery targets. Although small-molecule and peptide modulators dominate ion channel drug discovery, antibodies are emerging as an alternative modality. However, challenges persist in generating potent antibodies, especially for channels with limited extracellular epitopes. We herein present a bi-epitopic crosslinking strategy to overcome these challenges, focusing on Na V 1.7, a potential analgesic target. Aiming to crosslink two non-overlapping epitopes on voltage-sensing domains II and IV, we construct bispecific antibodies and ligand-antibody conjugates. Enhanced affinity and potency are observed in comparison to the monospecific controls. Among them, a ligand-antibody conjugate (1080-PEG 7 -ACDTB) displays a two-orders-of-magnitude improvement in potency (IC 50 of 0.06 ± 0.01 nM) and over 1,000-fold selectivity for Na V 1.7. Additionally, this conjugate demonstrates robust analgesic effects in mouse pain models. Our study introduces an approach to developing effective antibodies against Na V 1.7, thereby initiating a promising direction for the advancement of pain therapeutics.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; Peking University-Tsinghua University-National Institute Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 47.41 kDa 
  • Atom Count: 3,816 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 443 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of 1080 FabA [auth L]218Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of 1080 FabB [auth H]214Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 9 subunit alphaC [auth P]11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15858 (Homo sapiens)
Explore Q15858 
Go to UniProtKB:  Q15858
PHAROS:  Q15858
GTEx:  ENSG00000169432 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15858
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.965α = 90
b = 78.965β = 90
c = 147.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82373774

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-04
    Changes: Database references