9K3T | pdb_00009k3t

Cryo-EM structure of TMPRSS2 in complex with Fab fragments of 752 mAb and 2228 mAb

• PDB DOI: https://doi.org/10.2210/pdb9K3T/pdb
• EM Map EMD-62028: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Baculovirus transfer vector pFASTBAC1, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-10-20 Released: 2025-10-15 
• Deposition Author(s): Katsura, K., Hisano, T., Matsumoto, T., Shirouzu, M.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Monoclonal antibodies against human TMPRSS2 prevent infection by any SARS-CoV-2 variant

Harada, M., Matsumoto, T., Yamamoto, M., Goda, J., Idei, A., Ohtaki, K., Kojima, N., Yoneda, N., Miyauchi, K., Katsura, K., Ikeda, M., Hanada, K., Ishizuka-Katsura, Y., Hosaka, T., Hisano, T., Kaizuka, T., Yamamoto, T., Matsuda, M., Nakayama, M., Sugimoto-Ishige, A., Sakuma, M., Hashimoto, R., Takayama, K., Nakayama, M., Nguyen, C.T., Ishigaki, H., Itoh, Y., Hashizume, Y., Yoshida, M., Kawaguchi, Y., Takeda, M., Koseki, H., Shirouzu, M., Inoue, J.I., Saito, T.

(2025) iScience 28: 113424

• DOI: https://doi.org/10.1016/j.isci.2025.113424

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 140.16 kDa 
• Atom Count: 7,434 
• Modeled Residue Count: 967 
• Deposited Residue Count: 1,281 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	A	391	Homo sapiens	Mutation(s): 6  Gene Names: TMPRSS2, PRSS10 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393  Go to UniProtKB:  O15393
PHAROS:  O15393 GTEx:  ENSG00000184012

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 752 light chain	B [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 752 heavy chain	C [auth H]	229	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2228 light chain	D [auth l]	218	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2228 heavy chain	E [auth h]	230	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Katsura, K., Hisano, T., Matsumoto, T., Shirouzu, M.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release