8Z95 | pdb_00008z95

Humanized anti-PEG h6.3 Fab in complex with PEG

• PDB DOI: https://doi.org/10.2210/pdb8Z95/pdb

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


• Deposited: 2024-04-22 Released: 2025-02-12 
• Deposition Author(s): Lin, Y.C., Chang, C.Y., Su, Y.C.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.261 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

pH-Responsive Polyethylene Glycol Engagers for Enhanced Brain Delivery of PEGylated Nanomedicine to Treat Glioblastoma.

Meng, J.L., Dong, Z.X., Chen, Y.R., Lin, M.H., Liu, Y.C., Roffler, S.R., Lin, W.W., Chang, C.Y., Tzou, S.C., Cheng, T.L., Huang, H.C., Li, Z.Q., Lin, Y.C., Su, Y.C.

(2025) ACS Nano 19: 307-321

• PubMed: 39749925 
• DOI: https://doi.org/10.1021/acsnano.4c05906
• Primary Citation Related Structures: 
  8Z95


• PubMed Abstract: 
  

  The blood-brain barrier (BBB) remains a major obstacle for effective delivery of therapeutics to treat central nervous system (CNS) disorders. Although transferrin receptor (TfR)-mediated transcytosis is widely employed for brain drug delivery, the inefficient release of therapeutic payload hinders their efficacy from crossing the BBB. Here, we developed a pH-responsive anti-polyethylene glycol (PEG) × anti-TfR bispecific antibody (pH-PEG engager ^TfR ) that can complex with PEGylated nanomedicine at physiological pH to trigger TfR-mediated transcytosis in the brain microvascular endothelial cells, while rapidly dissociating from PEGylated nanomedicine at acidic endosomes for efficient release of PEGylated nanomedicine to cross the BBB. The pH-PEG engager ^TfR significantly increased the accumulation of PEGylated nanomedicine in the mouse brain compared to wild-type PEG engager ^TfR (WT-PEG engager ^TfR ). pH-PEG engager ^TfR -decorated PEGylated liposomal doxorubicin exhibited an enhanced antitumor effect and extended survival in a human glioblastoma (GBM) orthotopic xenograft mice model. Conditional release of PEGylated nanomedicine during BBB-related receptor-mediated transcytosis by pH-PEG engager ^TfR is promising for enhanced brain drug delivery to treat CNS disorders.

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Organizational Affiliation: 
• Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan.
Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.38 kDa 
• Atom Count: 6,790 
• Modeled Residue Count: 854 
• Deposited Residue Count: 876 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Anti-PEG antibody h6-3 Fab fragment	A, C [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Anti-PEG antibody h6-3 Fab fragment	B, D [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEU (Subject of Investigation/LOI)	E [auth A]	2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL C55 H112 O28 ISGUIIHZEJGUGQ-UHFFFAOYSA-N
IPA	F [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.261 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 245.365	α = 90
b = 43.574	β = 111.7
c = 110.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
HKL-2000	data collection
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Lin, Y.C., Chang, C.Y., Su, Y.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release