8RQF

Cryo-EM structure of human NTCP-Bulevirtide complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of antiviral drug bulevirtide bound to hepatitis B and D virus receptor protein NTCP.

Liu, H.Zakrzewicz, D.Nosol, K.Irobalieva, R.N.Mukherjee, S.Bang-Sorensen, R.Goldmann, N.Kunz, S.Rossi, L.Kossiakoff, A.A.Urban, S.Glebe, D.Geyer, J.Locher, K.P.

(2024) Nat Commun 15: 2476-2476

  • DOI: https://doi.org/10.1038/s41467-024-46706-w
  • Primary Citation of Related Structures:  
    8RQF

  • PubMed Abstract: 

    Cellular entry of the hepatitis B and D viruses (HBV/HDV) requires binding of the viral surface polypeptide preS1 to the hepatobiliary transporter Na + -taurocholate co-transporting polypeptide (NTCP). This interaction can be blocked by bulevirtide (BLV, formerly Myrcludex B), a preS1 derivative and approved drug for treating HDV infection. Here, to elucidate the basis of this inhibitory function, we determined a cryo-EM structure of BLV-bound human NTCP. BLV forms two domains, a plug lodged in the bile salt transport tunnel of NTCP and a string that covers the receptor's extracellular surface. The N-terminally attached myristoyl group of BLV interacts with the lipid-exposed surface of NTCP. Our structure reveals how BLV inhibits bile salt transport, rationalizes NTCP mutations that decrease the risk of HBV/HDV infection, and provides a basis for understanding the host specificity of HBV/HDV. Our results provide opportunities for structure-guided development of inhibitors that target HBV/HDV docking to NTCP.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/bile acid cotransporter349Homo sapiensMutation(s): 0 
Gene Names: SLC10A1NTCPGIG29
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14973 (Homo sapiens)
Explore Q14973 
Go to UniProtKB:  Q14973
PHAROS:  Q14973
GTEx:  ENSG00000100652 
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UniProt GroupQ14973
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of Fab3B [auth H]235Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of Fab3C [auth L]215Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab-specific nanobodyD [auth K]120Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PolymeraseE [auth B]46hepatitis B virus genotype CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q76R62 (Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-))
Explore Q76R62 
Go to UniProtKB:  Q76R62
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UniProt GroupQ76R62
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BJU (Subject of Investigation/LOI)
Query on BJU

Download Ideal Coordinates CCD File 
F [auth B]N-tetradecanoylglycine
C16 H31 N O3
DYUGTPXLDJQBRB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland214834
Swiss National Science FoundationSwitzerland189111
German Research Foundation (DFG)Germany197785619
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117372

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-23
    Changes: Data collection