9MQR | pdb_00009mqr

A8 Fab in complex with CD97


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MQR

This is version 1.1 of the entry. See complete history

Literature

Engineering antibody-drug conjugates targeting an adhesion GPCR, CD97.

Hattori, T.Wang, M.Corrado, A.D.Gross, S.Fang, M.Bang, I.Roy, N.Berezniuk, I.Donaldson, H.Groff, K.Ravn-Boess, N.Koide, A.Placantonakis, D.G.Park, C.Y.Koide, S.

(2025) Proc Natl Acad Sci U S A 122: e2516627122-e2516627122

  • DOI: https://doi.org/10.1073/pnas.2516627122
  • Primary Citation Related Structures: 
    9MQR

  • PubMed Abstract: 

    Adhesion G protein-coupled receptors (aGPCRs) are key cell-adhesion molecules involved in many cellular functions and contribute to human diseases, including cancer. aGPCRs are characterized by large extracellular regions that could serve as readily accessible antigens. However, the potential of aGPCRs as targets for biologic therapeutics has not been extensively explored. CD97, also known as ADGRE5, is an aGPCR that is upregulated in various cancer types, including acute myeloid leukemia (AML) and glioblastoma (GBM), and their respective cancer stem cells. Here, we developed antibody-drug conjugates (ADCs) targeting CD97 and assessed their efficacy against AML and GBM cells. We generated a panel of synthetic human antibodies targeting distinct epitopes of CD97, from which we identified an antibody that was efficiently internalized. This antibody binds to all isoforms of human CD97 but not to its close homolog, EMR2. Structure determination by single-particle cryo-electron microscopy revealed that this antibody targets the CD97 GPCR autoproteolysis-inducing (GAIN) domain, whose presence is conserved in aGPCRs, through an unconventional binding mode where it extensively utilizes the light chain framework for antigen recognition. Screening of conjugation methods and payloads resulted in a stable ADC that effectively killed AML and GBM cell lines, as well as patient-derived GBM stem cells, with minimal cytotoxicity against peripheral blood mononuclear cells from healthy donors. Our study demonstrates the therapeutic potential of targeting CD97, as well as the aGPCR GAIN domain in general, and uncovers a previously unrecognized surface that an antibody can utilize for antigen recognition.


  • Organizational Affiliation
    • Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016.

Macromolecule Content 

  • Total Structure Weight: 108.53 kDa 
  • Atom Count: 3,729 
  • Modeled Residue Count: 484 
  • Deposited Residue Count: 996 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adhesion G protein-coupled receptor E5542Homo sapiensMutation(s): 1 
Gene Names: ADGRE5CD97
UniProt & NIH Common Fund Data Resources
Find proteins for P48960 (Homo sapiens)
Explore P48960 
Go to UniProtKB:  P48960
PHAROS:  P48960
GTEx:  ENSG00000123146 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48960
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of A8 FabB [auth D]240Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of A8 FabC [auth E]214Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA251669

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references