8HLB

Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.

Akiba, H.Fujita, J.Ise, T.Nishiyama, K.Miyata, T.Kato, T.Namba, K.Ohno, H.Kamada, H.Nagata, S.Tsumoto, K.

(2023) Commun Biol 6: 987-987

  • DOI: https://doi.org/10.1038/s42003-023-05326-8
  • Primary Citation of Related Structures:  
    8HLB

  • PubMed Abstract: 

    Conventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different epitopes on the same antigen, thus altering crosslinking ability. In this study, we develop BpAbs against tumor necrosis factor receptor 2 (TNFR2), which is an attractive immune checkpoint target. Using different pairs of antibody variable regions specific to topographically distinct TNFR2 epitopes, we successfully regulate the size of BpAb-TNFR2 immunocomplexes to result in controlled agonistic activities. Our series of results indicate that the relative positions of the two epitopes recognized by the BpAb are critical for controlling its signaling activity. One particular antagonist, Bp109-92, binds TNFR2 in a 1:1 manner without unwanted signal transduction, and its structural basis is determined using cryo-electron microscopy. This antagonist suppresses the proliferation of regulatory T cells expressing TNFR2. Therefore, the BpAb format would be useful in designing specific and distinct antibody functions.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan. hakiba@pharm.kyoto-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 1B,Maltose/maltodextrin-binding periplasmic protein550Homo sapiensEscherichia coli K-12
This entity is chimeric
Mutation(s): 1 
Gene Names: TNFRSF1BTNFBRTNFR2malEb4034JW3994
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P20333 (Homo sapiens)
Explore P20333 
Go to UniProtKB:  P20333
GTEx:  ENSG00000028137 
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UniProt GroupsP20333P0AEX9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TR109 heavy chain236Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TR109 light chain218Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TR92 heavy chain238Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TR92 light chain214Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP22ak0101099
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101117
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121003
Japan Agency for Medical Research and Development (AMED)JapanJP17pc0101020
Japan Science and TechnologyJapanJPMJOP1861
Japan Society for the Promotion of Science (JSPS)JapanJP21K06453
Japan Society for the Promotion of Science (JSPS)JP20K22630
Kyoto University FoundationJapan--
Takeda Science FoundationJapan--
JEOL YOKOGUSHI Research Alliance Laboratories of Osaka UniversityJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release