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), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (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 of 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.

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 
• Modelled 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
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (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