7DF1

Crystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4 scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice.

Tian, X.Liu, X.Ding, J.Wang, F.Wang, K.Liu, J.Wei, Z.Hao, X.Li, Y.Wei, X.Zhang, H.Sui, J.

(2022) Nat Biomed Eng 

  • DOI: https://doi.org/10.1038/s41551-022-00956-5
  • Primary Citation of Related Structures:  
    7DF1

  • PubMed Abstract: 

    The cell-surface glycoprotein CD98-a subunit of the LAT1/CD98 amino acid transporter-is an attractive target for cancer immunotherapies, but its widespread expression has hampered the development of CD98-targeting antibody therapeutics. Here we report that an anti-CD98 antibody, identified via the screening of phage-display libraries of CD98 single-chain variable fragments with mutated complementarity-determining regions, preserves the physiological function of CD98 and elicits broad-spectrum crystallizable-fragment (Fc)-mediated anti-tumour activity (requiring Fcγ receptors for immunoglobulins, macrophages, dendritic cells and CD8 + T cells, as well as other components of the innate and adaptive immune systems) in multiple xenograft and syngeneic tumour models established in CD98-humanized mice. We also show that a variant of the anti-CD98 antibody with pH-dependent binding, generated by solving the structure of the antibody-CD98 complex, displayed enhanced tumour-specific activity and pharmacokinetics. pH-dependent antibody variants targeting widely expressed antigens may lead to superior therapeutic outcomes.


  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4F2 cell-surface antigen heavy chain
A, B, C, D
420Homo sapiensMutation(s): 0 
Gene Names: SLC3A2MDU1
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens)
Explore P08195 
Go to UniProtKB:  P08195
PHAROS:  P08195
GTEx:  ENSG00000168003 
Entity Groups  
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UniProt GroupP08195
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S1-F4 VHE [auth H],
G [auth E],
I [auth F],
K [auth G]
140Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IGL c2062_light_IGKV4-1_IGKJ5F [auth L],
H [auth I],
J,
L [auth K]
122Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A5C2G3X0 (Homo sapiens)
Explore A0A5C2G3X0 
Go to UniProtKB:  A0A5C2G3X0
Entity Groups  
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UniProt GroupA0A5C2G3X0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.802α = 90
b = 165.212β = 90
c = 176.191γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description