9IP7 | pdb_00009ip7

Local refinement structure of sEGFR and 528 Fv (from HL-type bispecific diabody Ex3) complex

• PDB DOI: https://doi.org/10.2210/pdb9IP7/pdb
• EM Map EMD-60764: EMDB EMDataResource

• Classification: ANTITUMOR PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Cricetulus griseus, Brevibacillus choshinensis
• Mutation(s): No 


• Deposited: 2024-07-10 Released: 2025-05-28 
• Deposition Author(s): Sato, K., Uehara, S., Tsugita, A., Matsui, T., Asano, R., Makabe, K., Yokoyama, T., Tanaka, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement.

Sato, K., Uehara, S., Tsugita, A., Ishii, M., Ishiyama, S., Maejima, A., Nakahara, I., Nazuka, M., Matsui, T., Christos, G., Yokoyama, T., Kumagai, I., Makabe, K., Asano, R., Tanaka, Y.

(2025) Cell Rep 44: 115965-115965

• PubMed: 40664209 
• DOI: https://doi.org/10.1016/j.celrep.2025.115965
• Primary Citation Related Structures: 
  9IP7, 9IP8, 9IP9, 9IPA, 9IPB, 9IPC, 9IPD, 9IPE


• PubMed Abstract: 
  

  Bispecific antibodies (BsAbs) have been developed as anti-cancer drugs that accumulate activated T cells on cancer cells by bridging the antigens present in each cell. Ex3 is a diabody-type BsAb composed of an anti-epidermal growth factor receptor (EGFR) antibody and an anti-CD3 antibody. In the design of Ex3, the LH-type domain order (Ex3LH) is shown to have more than 100-fold greater anti-cancer activity than the HL-type domain order (Ex3HL). To understand this phenomenon of activity enhancement by domain-order rearrangement, we report here cryoelectron microscopy (cryo-EM) structures of both Ex3HL and Ex3LH in complex with EGFR and CD3. A structural comparison of the HL and LH types reveals that the domain rearrangement leads to drastic structural changes and that the avoidance of steric hindrance by a favorable bridging angle on the cell surface is the fundamental mechanism for this activity enhancement.

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Organizational Affiliation: 
• Graduate School of Life Sciences, Tohoku University, Miyagi 980-8577, Japan.
Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.
Graduate School of Science and Engineering, Yamagata University, Yamagata 992-8510, Japan.
Graduate School of Life Sciences, Tohoku University, Miyagi 980-8577, Japan; School of Science, Kitasato University, Minato City, Tokyo 108-8641, Japan.
Center for Soft Nanoscience, Institute for Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany.
Graduate School of Life Sciences, Tohoku University, Miyagi 980-8577, Japan; The Advanced Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, Miyagi 980-8573, Japan.
Graduate School of Science and Engineering, Yamagata University, Yamagata 992-8510, Japan. Electronic address: [e-mail].
Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan. Electronic address: [e-mail].
Graduate School of Life Sciences, Tohoku University, Miyagi 980-8577, Japan; The Advanced Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, Miyagi 980-8573, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 97.88 kDa 
• Atom Count: 5,809 
• Modeled Residue Count: 738 
• Deposited Residue Count: 882 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	627	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
PHAROS:  P00533 GTEx:  ENSG00000146648
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P00533-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
528 Fv from HL-type bispecific diabody Ex3	B [auth D]	255	synthetic construct	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Sato, K., Uehara, S., Tsugita, A., Matsui, T., Asano, R., Makabe, K., Yokoyama, T., Tanaka, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Data collection
• Version 1.2: 2025-07-30
  Changes: Data collection, Database references
• Version 1.3: 2025-08-06
  Changes: Data collection, Database references