8B7D

Luminal domain of TMEM106B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry.

Baggen, J.Jacquemyn, M.Persoons, L.Vanstreels, E.Pye, V.E.Wrobel, A.G.Calvaresi, V.Martin, S.R.Roustan, C.Cronin, N.B.Reading, E.Thibaut, H.J.Vercruysse, T.Maes, P.De Smet, F.Yee, A.Nivitchanyong, T.Roell, M.Franco-Hernandez, N.Rhinn, H.Mamchak, A.A.Ah Young-Chapon, M.Brown, E.Cherepanov, P.Daelemans, D.

(2023) Cell 186: 3427

  • DOI: https://doi.org/10.1016/j.cell.2023.06.005
  • Primary Citation of Related Structures:  
    8B7D

  • PubMed Abstract: 

    SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.


  • Organizational Affiliation

    KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium. Electronic address: jim.baggen@kuleuven.be.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 106B199Homo sapiensMutation(s): 0 
Gene Names: TMEM106B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUM4 (Homo sapiens)
Explore Q9NUM4 
Go to UniProtKB:  Q9NUM4
PHAROS:  Q9NUM4
GTEx:  ENSG00000106460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUM4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.408α = 90
b = 52.408β = 90
c = 132.922γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001061
Wellcome TrustUnited KingdomFC001061
Medical Research Council (MRC, United Kingdom)United KingdomFC001061
The Francis Crick InstituteUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references