9OPR | pdb_00009opr

TMPRSS2 S441A in complex with the H1H7 Fab and anti-kappa light chain nanobody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9OPR

This is version 1.0 of the entry. See complete history

Literature

TMPRSS2-mediated coronavirus spike activation and inhibition.

McCallum, M.Case, J.B.Brown, J.T.Park, Y.J.Lee, J.Sutherland, E.Aggarwal, A.Gibson, C.Lempp, F.A.Stewart, C.Tortorici, M.A.Sanapala, S.Low, J.S.Asarnow, D.Bohan, D.Dellota Jr., E.Merz, B.Chawla, B.Kar, S.Lanzavecchia, A.Sallusto, F.Riley, N.M.Turville, S.Purcell, L.Diamond, M.S.Veesler, D.

(2026) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-026-01801-y
  • Primary Citation Related Structures: 
    11HK, 11HL, 11HN, 11HW, 9OPQ, 9OPR, 9YYU, 9YYV, 9Z3J, 9Z3K

  • PubMed Abstract: 

    The protease TMPRSS2 facilitates coronavirus infections, yet its mechanism of viral glycoprotein recognition remains unclear. Here we show that, following ACE2 engagement of the SARS-CoV-2 spike (S) inducing the early fusion intermediate conformation (E-FIC), TMPRSS2 cleaves the R815 S 2 ' site and promotes fusogenic conformational changes leading to viral entry. We unveil TMPRSS2 recognition of S 2 ', identify key residues modulating binding specificity and demonstrate that S 2 ' site-directed broadly neutralizing antibodies target E-FIC and inhibit viral entry by blocking TMPRSS2 access. We computationally designed stabilized E-FIC as a vaccine candidate, overcoming the transient nature of this state. We describe a TMPRSS2-directed monoclonal antibody inhibiting several coronaviruses, including SARS-CoV-2 variants and protecting mice against SARS-CoV-2 challenge. These results outline the mechanistic role of TMPRSS2 and S 2 ' site-directed antibodies in coronavirus entry.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 124.12 kDa 
  • Atom Count: 6,517 
  • Modeled Residue Count: 886 
  • Deposited Residue Count: 1,124 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane protease serine 2533Homo sapiensMutation(s): 6 
Gene Names: SMT3YDR510WD9719.15TMPRSS2PRSS10
EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
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 GroupsQ12306O15393
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q12306-1O15393-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
H1H7 antibody heavy chainB [auth H]220Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
H1H7 antibody light chainC [auth L]212Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-kappa light chain nanobodyD [auth N]159Lama glamaMutation(s): 0 

Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth B]2N-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release