8G0M | pdb_00008g0m

Structure of complex between TV6.6 and CD98hc ECD

• PDB DOI: https://doi.org/10.2210/pdb8G0M/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-01-31 Released: 2023-10-18 
• Deposition Author(s): Kariolis, M.S., Lexa, K., Liau, N.P.D., Srivastava, D., Tran, H., Wells, R.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 

Starting Model: experimental

Literature

CD98hc is a target for brain delivery of biotherapeutics.

Chew, K.S., Wells, R.C., Moshkforoush, A., Chan, D., Lechtenberg, K.J., Tran, H.L., Chow, J., Kim, D.J., Robles-Colmenares, Y., Srivastava, D.B., Tong, R.K., Tong, M., Xa, K., Yang, A., Zhou, Y., Akkapeddi, P., Annamalai, L., Bajc, K., Blanchette, M., Cherf, G.M., Earr, T.K., Gill, A., Huynh, D., Joy, D., Knight, K.N., Lac, D., Leung, A.W., Lexa, K.W., Liau, N.P.D., Becerra, I., Malfavon, M., McInnes, J., Nguyen, H.N., Lozano, E.I., Pizzo, M.E., Roche, E., Sacayon, P., Calvert, M.E.K., Daneman, R., Dennis, M.S., Duque, J., Gadkar, K., Lewcock, J.W., Mahon, C.S., Meisner, R., Solanoy, H., Thorne, R.G., Watts, R.J., Zuchero, Y.J.Y., Kariolis, M.S.

(2023) Nat Commun 14: 5053-5053

• PubMed: 37598178 
• DOI: https://doi.org/10.1038/s41467-023-40681-4
• Primary Citation Related Structures: 
  8G0M


• PubMed Abstract: 
  

  Brain exposure of systemically administered biotherapeutics is highly restricted by the blood-brain barrier (BBB). Here, we report the engineering and characterization of a BBB transport vehicle targeting the CD98 heavy chain (CD98hc or SLC3A2) of heterodimeric amino acid transporters (TV ^CD98hc ). The pharmacokinetic and biodistribution properties of a CD98hc antibody transport vehicle (ATV ^CD98hc ) are assessed in humanized CD98hc knock-in mice and cynomolgus monkeys. Compared to most existing BBB platforms targeting the transferrin receptor, peripherally administered ATV ^CD98hc demonstrates differentiated brain delivery with markedly slower and more prolonged kinetic properties. Specific biodistribution profiles within the brain parenchyma can be modulated by introducing Fc mutations on ATV ^CD98hc that impact FcγR engagement, changing the valency of CD98hc binding, and by altering the extent of target engagement with Fabs. Our study establishes TV ^CD98hc as a modular brain delivery platform with favorable kinetic, biodistribution, and safety properties distinct from previously reported BBB platforms.

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Organizational Affiliation: 
• Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA.
Department of Pharmacology, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, CA, USA.
Department of Neurosciences, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, CA, USA.
Department of Pharmaceutics, University of Minnesota, Minneapolis, MN, USA.
Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA. [e-mail].
Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA. [e-mail].

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: 74.64 kDa 
• Atom Count: 5,180 
• Modeled Residue Count: 620 
• Deposited Residue Count: 652 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4F2 cell-surface antigen heavy chain	A	425	Homo sapiens	Mutation(s): 0  Gene Names: SLC3A2, MDU1
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens) Explore P08195  Go to UniProtKB:  P08195
PHAROS:  P08195 GTEx:  ENSG00000168003

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TV 6.6 Fc fragment	B	227	synthetic construct	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G61334IA GlyCosmos: G61334IA GlyGen: G61334IA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	D [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.152	α = 90
b = 167.126	β = 90
c = 83.677	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Kariolis, M.S., Lexa, K., Liau, N.P.D., Srivastava, D., Tran, H., Wells, R.C.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary