7VAG

Cryo-EM structure of human NTCP complexed with YN69202Fab in the presence of myristoylated preS1 peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the bile acid transporter and HBV receptor NTCP.

Asami, J.Kimura, K.T.Fujita-Fujiharu, Y.Ishida, H.Zhang, Z.Nomura, Y.Liu, K.Uemura, T.Sato, Y.Ono, M.Yamamoto, M.Noda, T.Shigematsu, H.Drew, D.Iwata, S.Shimizu, T.Nomura, N.Ohto, U.

(2022) Nature 606: 1021-1026

  • DOI: https://doi.org/10.1038/s41586-022-04845-4
  • Primary Citation of Related Structures:  
    7VAD, 7VAE, 7VAF, 7VAG, 7WSI

  • PubMed Abstract: 

    Chronic infection with hepatitis B virus (HBV) affects more than 290 million people worldwide, is a major cause of cirrhosis and hepatocellular carcinoma, and results in an estimated 820,000 deaths annually 1,2 . For HBV infection to be established, a molecular interaction is required between the large glycoproteins of the virus envelope (known as LHBs) and the host entry receptor sodium taurocholate co-transporting polypeptide (NTCP), a sodium-dependent bile acid transporter from the blood to hepatocytes 3 . However, the molecular basis for the virus-transporter interaction is poorly understood. Here we report the cryo-electron microscopy structures of human, bovine and rat NTCPs in the apo state, which reveal the presence of a tunnel across the membrane and a possible transport route for the substrate. Moreover, the cryo-electron microscopy structure of human NTCP in the presence of the myristoylated preS1 domain of LHBs, together with mutation and transport assays, suggest a binding mode in which preS1 and the substrate compete for the extracellular opening of the tunnel in NTCP. Our preS1 domain interaction analysis enables a mechanistic interpretation of naturally occurring HBV-insusceptible mutations in human NTCP. Together, our findings provide a structural framework for HBV recognition and a mechanistic understanding of sodium-dependent bile acid translocation by mammalian NTCPs.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/bile acid cotransporter343Homo sapiensMutation(s): 1 
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
Fab heavy chain from antibody IgG clone number YN69202B [auth H]249Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain from antibody IgG clone number YN69202C [auth L]219Mus musculusMutation(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: 3.32 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)Japan19H03164
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H00976

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2022-07-13
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary