8HRX

Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of hepatitis B virus receptor binding.

Asami, J.Park, J.H.Nomura, Y.Kobayashi, C.Mifune, J.Ishimoto, N.Uemura, T.Liu, K.Sato, Y.Zhang, Z.Muramatsu, M.Wakita, T.Drew, D.Iwata, S.Shimizu, T.Watashi, K.Park, S.Y.Nomura, N.Ohto, U.

(2024) Nat Struct Mol Biol 31: 447-454

  • DOI: https://doi.org/10.1038/s41594-023-01191-5
  • Primary Citation of Related Structures:  
    8HRX, 8HRY

  • PubMed Abstract: 

    Hepatitis B virus (HBV), a leading cause of developing hepatocellular carcinoma affecting more than 290 million people worldwide, is an enveloped DNA virus specifically infecting hepatocytes. Myristoylated preS1 domain of the HBV large surface protein binds to the host receptor sodium-taurocholate cotransporting polypeptide (NTCP), a hepatocellular bile acid transporter, to initiate viral entry. Here, we report the cryogenic-electron microscopy structure of the myristoylated preS1 (residues 2-48) peptide bound to human NTCP. The unexpectedly folded N-terminal half of the peptide embeds deeply into the outward-facing tunnel of NTCP, whereas the C-terminal half formed extensive contacts on the extracellular surface. Our findings reveal an unprecedented induced-fit mechanism for establishing high-affinity virus-host attachment and provide a blueprint for the rational design of anti-HBV drugs targeting virus entry.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/bile acid cotransporter343Homo sapiensMutation(s): 0 
Gene Names: NTCP
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14973
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PreS1 protein (Fragment)55Hepatitis B virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q67926 (Hepatitis B virus genotype B2 subtype adw (isolate China/patient4/1996))
Explore Q67926 
Go to UniProtKB:  Q67926
Entity Groups  
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UniProt GroupQ67926
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chain from antibody IgG clone number YN9048C [auth H]246Ondatra zibethicusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain from antibody IgG clone number YN9048D [auth L]214Ondatra zibethicusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan22H02556

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection, Structure summary