8RQF | pdb_00008rqf

Cryo-EM structure of human NTCP-Bulevirtide complex

• PDB DOI: https://doi.org/10.2210/pdb8RQF/pdb
• EM Map EMD-19440: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Lama glama, hepatitis B virus genotype C
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-01-18 Released: 2024-03-27 
• Deposition Author(s): Liu, H., Zakrzewicz, D., Nosol, K., Irobalieva, R.N., Mukherjee, S., Bang-Soerensen, R., Goldmann, N., Kunz, S., Rossi, L., Kossiakoff, A.A., Urban, S., Glebe, D., Geyer, J., Locher, K.P.
• Funding Organization(s): Swiss National Science Foundation, German Research Foundation (DFG), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 38509088 
• DOI: https://doi.org/10.1038/s41467-024-46706-w
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany.
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Justus Liebig University Giessen, Giessen, Germany.
German Center for Infection Research (DZIF) - Giessen-Marburg-Langen Partner Site, Giessen, Germany.
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. [e-mail].
Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany. [e-mail].
German Center for Infection Research (DZIF) - partner site Heidelberg, Heidelberg, Germany. [e-mail].
Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Justus Liebig University Giessen, Giessen, Germany. [e-mail].
German Center for Infection Research (DZIF) - Giessen-Marburg-Langen Partner Site, Giessen, Germany. [e-mail].
Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany. [e-mail].
Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 105.37 kDa 
• Atom Count: 6,950 
• Modeled Residue Count: 903 
• Deposited Residue Count: 965 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/bile acid cotransporter	A	349	Homo sapiens	Mutation(s): 0  Gene Names: SLC10A1, NTCP, GIG29 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab3	B [auth H]	235	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab3	C [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-specific nanobody	D [auth K]	120	Lama glama	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase	E [auth B]	46	hepatitis B virus genotype C	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BJU (Subject of Investigation/LOI)	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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Liu, H., Zakrzewicz, D., Nosol, K., Irobalieva, R.N., Mukherjee, S., Bang-Soerensen, R., Goldmann, N., Kunz, S., Rossi, L., Kossiakoff, A.A., Urban, S., Glebe, D., Geyer, J., Locher, K.P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	214834
Swiss National Science Foundation	Switzerland	189111
German Research Foundation (DFG)	Germany	197785619
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117372

Revision History  

• 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