9K3T | pdb_00009k3t

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 113424-113424

  • DOI: https://doi.org/10.1016/j.isci.2025.113424
  • Primary Citation of Related Structures:  
    9K3T

  • PubMed Abstract: 

    The transmembrane serine protease 2 (TMPRSS2) plays a critical role in SARS-CoV-2 infection by priming the viral Spike (S) protein for host cell entry and thus represents a potential target for COVID-19 therapy. Here monoclonal antibodies (mAbs) against human TMPRSS2 were established for therapeutic application. In vitro infection by SARS-CoV-2 of cell lines and human lung organoids was strongly inhibited by the TMPRSS2 mAbs. These mAbs inhibited infection of all SARS-CoV-2 variants tested including omicron. mAbs recognized epitopes different from the enzymatic active site and did not inhibit protease activity, suggesting blockade of steric interactions of S protein-ACE2/TMPRSS2. The inhibitory activity of the mAbs in vivo was examined in human ACE2 / TMPRSS2 -double knock-in mouse and macaque models. Analysis of viral titers and histopathological analysis of the lung in these infected animals indicated that the TMPRSS2 mAb effectively suppressed viral titers and induction of inflammation in vivo .


  • Organizational Affiliation
    • Drug Discovery Antibody Platform Unit, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 2391Homo sapiensMutation(s): 6 
Gene Names: TMPRSS2PRSS10
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15393
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 752 light chainB [auth L]213Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 752 heavy chainC [auth H]229Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 2228 light chainD [auth l]218Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 2228 heavy chainE [auth h]230Mus musculusMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Data collection, Database references