9GFL | pdb_00009gfl

Crystal structure of ASO binding Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.248 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Improved targeted delivery of antisense oligonucleotide with an antibody mask.

Hsia, H.E.Zanini, C.Simonneau, C.Fraidling, J.Kraft, T.E.Mayer, K.Sommer, A.Indlekofer, A.Wirth, T.Benz, J.Georges, G.Langer, L.M.Gassner, C.Larraillet, V.Lohmann, S.Koller, E.Manso, M.Ravn, J.Hofer, K.Emrich, T.Niewohner, J.Schumacher, F.Brinkmann, U.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf487
  • Primary Citation of Related Structures:  
    9GF5, 9GFD, 9GFJ, 9GFL

  • PubMed Abstract: 

    Antisense oligonucleotides (ASOs) are synthetic nucleic acid strands designed to modulate gene expression by binding to RNA transcripts. In brain diseases, transferrin receptor (TfR)-targeting antibody-ASO conjugates have shown promise for brain delivery of ASOs via transcytosis in preclinical studies. This enables the more patient friendly intravenous or subcutaneous administration of the compounds. However, these conjugates can exhibit faster plasma clearance and different peripheral pharmacokinetic profiles due to ASO modifications, such as phosphorothioate (PS) linkages and locked nucleic acids (LNAs). In this study, we employed an antibody recognizing LNA- and PS-modified ASOs independent of the base sequences as a cloaking module to mitigate these issues. Using Kutzneria albida transglutaminase (KTG) technology and click chemistry, we generated TfR antibody-ASO conjugates with covalently or noncovalently incorporated ASO binders. Additionally, a noncovalent carrier antibody approach was explored. These conjugates and complexes with additional ASO binder(s) show improved TfR-targeted cellular uptake, undergo transcytosis in cellular blood-brain barrier models, show less nonspecific cellular accumulation, and anticipated ASO activity.


  • Organizational Affiliation
    • Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg82377, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment heavy chainA [auth H]226Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment light chainB [auth L]219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
F [auth H],
H [auth L]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth H],
D [auth H],
E [auth H],
I [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.248 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.171α = 90
b = 59.615β = 94.62
c = 62.692γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references