6I9Q | pdb_00006i9q

Structure of the mouse CD98 heavy chain ectodomain

• PDB DOI: https://doi.org/10.2210/pdb6I9Q/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-11-24 Released: 2019-04-17 
• Deposition Author(s): Schiefner, A., Deuschle, F.-C., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.218 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structural differences between the ectodomains of murine and human CD98hc.

Deuschle, F.C., Schiefner, A., Skerra, A.

(2019) Proteins 87: 693-698

• PubMed: 30958588 
• DOI: https://doi.org/10.1002/prot.25686
• Primary Citation Related Structures: 
  6I9Q


• PubMed Abstract: 
  

  The CD98 heavy chain (CD98hc) constitutes both a promising cell surface target for the treatment of cancers and a transcytosis receptor potentially useful for the brain delivery of therapeutics. However, pharmacokinetic studies and safety assessment of cognate antibodies or nonimmunoglobulin binding proteins in rodents is hampered by cross-species variability of both amino acid sequence and glycosylation pattern. Here, we report the crystal structure of the murine CD98hc extracellular domain and a comprehensive comparison with its human ortholog, revealing only one conserved surface patch that is neither shielded by glycosylation nor by the cell membrane with an accessible surface area typical for an antibody epitope. Our results imply the necessity of a surrogate approach for CD98hc-specific binding proteins with predictive power for clinical investigations.

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Organizational Affiliation: 
• Lehrstuhl für Biologische Chemie, Technische Universität München, Freising, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.53 kDa 
• Atom Count: 3,545 
• Modeled Residue Count: 422 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4F2 cell-surface antigen heavy chain	A	434	Mus musculus	Mutation(s): 0  Gene Names: Slc3a2, Mdu1
UniProt
Find proteins for P10852 (Mus musculus) Explore P10852  Go to UniProtKB:  P10852

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.218 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.384	α = 90
b = 97.384	β = 90
c = 218.98	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Schiefner, A., Deuschle, F.-C., Skerra, A.

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description