9GFJ | pdb_00009gfj

Crystal structure of ASO binding Fab fragment with ASO143

PDB DOI: https://doi.org/10.2210/pdb9GFJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-09 Released: 2025-08-20
Deposition Author(s): Hsia, H.-E., Zanini, C., Simonneau, C., Fraidling, J., Kraft, T., Mayer, K., Sommer, A., Indlekofer, A., Wirht, T., Benz, J., Georges, G., Langer, L.M., Gassner, C., Larraillet, V., Manso, M., Ravn, J., Hofer, K., Emrich, T., Niewoehner, J., Schumacher, F., Brinkmann, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 41166443 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaf487
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 49.69 kDa
Atom Count: 3,865
Modeled Residue Count: 428
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment light chain	B [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IKV (Subject of Investigation/LOI) Query on A1IKV Download:Ideal Coordinates CCD File SDF format, chain L MOL2 format, chain L mmCIF format, chain L	L	1-[(1~{S},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-3-(6-aminopurin-9-yl)-7-[[(1~{R},3~{R},4~{R},7~{S})-3-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-3-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-3-yl]-5-methyl-pyrimidine-2,4-dione C₄₄ H₅₄ N₁₃ O₂₃ P₃ S₃ NZVZIQVDJJVXQQ-SSOWSIFGSA-N		Interactions Focus chain L Interactions & Density Focus chain L
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain F [auth H] SDF format, chain G [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain H [auth L] SDF format, chain E [auth H] SDF format, chain D [auth H] MOL2 format, chain C [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain H [auth L] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] mmCIF format, chain C [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain H [auth L] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H]	C [auth H] D [auth H] E [auth H] F [auth H] G [auth L] C [auth H], D [auth H], E [auth H], F [auth H], G [auth L], H [auth L], J [auth L], K [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth L]