8JYQ | pdb_00008jyq

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with epitope peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.233 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8JYQ

This is version 1.3 of the entry. See complete history

Literature

Locally misfolded HER2 expressed on cancer cells is a promising target for development of cancer-specific antibodies.

Arimori, T.Mihara, E.Suzuki, H.Ohishi, T.Tanaka, T.Kaneko, M.K.Takagi, J.Kato, Y.

(2024) Structure 32: 536-549.e5

  • DOI: https://doi.org/10.1016/j.str.2024.02.007
  • Primary Citation Related Structures: 
    8JYQ, 8JYR

  • PubMed Abstract: 

    Overexpression of human epidermal growth factor receptor 2 (HER2) in breast and gastric cancers is associated with a poor prognosis, making it an important therapeutic target. Here, we establish a novel cancer-specific anti-HER2 antibody, H 2 Mab-214. H 2 Mab-214 reacts with HER2 on cancer cells, but unlike the therapeutic antibody trastuzumab, it does not react with HER2 on normal cells in flow cytometry measurements. A crystal structure suggests that H 2 Mab-214 recognizes a structurally disrupted region in the HER2 domain IV, which normally forms a β-sheet. We show that this misfolding is inducible by site-directed mutagenesis mimicking the disulfide bond defects that also may occur in cancer cells, indicating that the local misfolding in the Cys-rich domain IV governs the cancer-specificity of H 2 Mab-214. Furthermore, we show that H 2 Mab-214 effectively suppresses tumor growth in xenograft mouse models. Our findings offer a potential strategy for developing cancer-specific therapeutic antibodies that target partially misfolded cell surface receptors.


  • Organizational Affiliation
    • Institute for Protein Research, Osaka University, 3-2. Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address: arimori@protein.osaka-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 79.47 kDa 
  • Atom Count: 5,592 
  • Modeled Residue Count: 673 
  • Deposited Residue Count: 704 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H2CasMab-1 VH(S112C),SARAH
A, D
174Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
H2CasMab-1 VL,SARAH(S37C)
B, E
170Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
H2CasMab-1 epitope peptide
C, F
8Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
PHAROS:  P04626
GTEx:  ENSG00000141736 
Entity Groups
UniProt GroupP04626
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.233 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.143α = 90
b = 62.793β = 94.419
c = 78.122γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H02416
Japan Agency for Medical Research and Development (AMED)Japan20am0101075

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary