9JD1 | pdb_00009jd1

Crystal structure of TMPRSS2 in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

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


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Literature

The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies.

Zhao, Z.Yang, Q.Liu, X.Li, M.Duan, Y.Du, M.Zhou, A.Liu, H.He, Y.Wang, W.Lu, Y.Zhang, X.Wang, H.Yang, X.Zhang, H.Chen, X.Rao, Z.Yang, H.

(2025) Nat Commun 16: 6636-6636

  • DOI: https://doi.org/10.1038/s41467-025-62023-2
  • Primary Citation of Related Structures:  
    9JCX, 9JCY, 9JD0, 9JD1, 9U8G

  • PubMed Abstract: 

    HCoV-HKU1, one of seven human coronaviruses (HCoVs) that have harmful effects on human health, accounts for a substantial portion of common cold cases and can cause severe respiratory diseases in certain populations. Currently, effective antiviral treatments against this virus are limited. Recently, TMPRSS2, a host protease long acknowledged for its role in priming the spike proteins of various CoVs and promoting viral entry, was identified as a functional receptor for HCoV-HKU1, opening an avenue for anti-HCoV-HKU1 therapy development. In this study, we elucidate the detailed molecular mechanism underlying the interaction between the HCoV-HKU1 receptor-binding domain (RBD) and TMPRSS2 via crystallography. Guided by these structural insights, we successfully develop two types of therapeutic antibodies against HCoV-HKU1. The first type neutralizes the RBD, potently disrupting its interaction with TMPRSS2 and preventing viral infection. The second type targets TMPRSS2, inhibiting its enzymatic activity and/or interfering with its binding to the RBD. The latter demonstrates broad-spectrum anti-CoV activity, as the enzymatic activity of TMPRSS2 is crucial for both HCoV-HKU1 infection and other CoV infections. Our findings provide crucial structural insights into the recognition of TMPRSS2 by HCoV-HKU1 and offer promising antibody-based strategies for combating HCoV-HKU1 and other CoV infections.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 2 catalytic chainA [auth D]249Homo sapiensMutation(s): 0 
Gene Names: TMPRSS2PRSS10
EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens)
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Go to UniProtKB:  O15393
PHAROS:  O15393
GTEx:  ENSG00000184012 
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UniProt GroupO15393
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of FabB [auth A]217Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of FabC [auth B]240Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 2 non-catalytic chainD [auth C]146Homo sapiensMutation(s): 5 
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O15393-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
5N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.164α = 90
b = 89.176β = 90
c = 201.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92169109

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release