9LY6 | pdb_00009ly6

antibody 20G5 (Fab')2 in complex with human B7-H3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9LY6

This is version 1.2 of the entry. See complete history

Literature

B7-H3-mediated cis-inhibition of EGFR by a tumor-selective bispecific antibody enhances anti-tumor efficacy and minimizes toxicities.

Guan, J.Chia, T.Li, B.Zhu, T.Liao, Z.Deng, J.Fu, F.Wu, W.Liu, C.Liu, Y.Li, N.Yue, L.Cao, L.Lu, J.Zhu, M.Ling, X.Zheng, H.Lin, S.Li, L.Zhou, S.He, K.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69703-7
  • Primary Citation Related Structures: 
    9LY5, 9LY6

  • PubMed Abstract: 

    Therapeutic targeting of epidermal growth factor receptor (EGFR) in solid tumors faces significant limitations due to on-target/off-tumor toxicities, underscoring the urgent need for tumor-selective anti-EGFR therapies. Comprehensive bioinformatics and histopathological analyses identify marked upregulation of B7-H3 across EGFR-positive malignancies, contrasting with its minimal expression in healthy tissues. Leveraging an unbiased functional screen of bispecific antibodies (bsAbs) combining diverse B7-H3 and EGFR binders, we develop IBI334, a EGFR/B7-H3 bsAb exhibiting exceptional tumor selectivity. In preclinical models, IBI334 outperforms conventional EGFR antibodies by demonstrating superior EGFR occupancy, enhanced ligand-blocking efficacy, accelerated receptor degradation, and potent suppression of downstream EGFR signaling. Mechanistic studies demonstrate B7-H3-mediated cis-inhibition. The human B7-H3 extracellular domain (ECD) in complex with anti-B7-H3 Fab is resolved by cryo-EM, revealing critical residues for the antibody-B7-H3 interaction. IBI334 demonstrates robust antitumor activity in vitro and in vivo across EGFR-driven tumor models and synergized effectively with KRAS inhibitors. Toxicological evaluations in non-human primates reveals a favorable safety profile, with no EGFR-related adverse effects observed at doses up to 120 mg/kg over 4 weeks. Supported by these preclinical findings, IBI334 has advanced to a phase 1 clinical trial (NCT05774873) for advanced/metastatic solid tumors.


  • Organizational Affiliation
    • Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China.

Macromolecule Content 

  • Total Structure Weight: 143.68 kDa 
  • Atom Count: 9,196 
  • Modeled Residue Count: 1,208 
  • Deposited Residue Count: 1,333 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD276 antigen433Homo sapiensMutation(s): 0 
Gene Names: CD276B7H3PSEC0249UNQ309/PRO352
UniProt & NIH Common Fund Data Resources
Find proteins for Q5ZPR3 (Homo sapiens)
Explore Q5ZPR3 
Go to UniProtKB:  Q5ZPR3
PHAROS:  Q5ZPR3
GTEx:  ENSG00000103855 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZPR3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
antibody 20G5 Fab heavy chain
B, D
237Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
antibody 20G5 Fab light chain
C, E
213Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Data collection, Database references
  • Version 1.2: 2026-04-15
    Changes: Data collection, Database references