8XCD | pdb_00008xcd

Macaca fascicularis NTCP in complex with YN69083 Fab

• PDB DOI: https://doi.org/10.2210/pdb8XCD/pdb
• EM Map EMD-38240: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN/IMMUNE SYSTEM
• Organism(s): Macaca fascicularis, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-12-08 Released: 2024-11-13 
• Deposition Author(s): Park, J.H., Ishimoto, N., Park, S.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis for hepatitis B virus restriction by a viral receptor homologue.

Shionoya, K., Park, J.H., Ekimoto, T., Takeuchi, J.S., Mifune, J., Morita, T., Ishimoto, N., Umezawa, H., Yamamoto, K., Kobayashi, C., Kusunoki, A., Nomura, N., Iwata, S., Muramatsu, M., Tame, J.R.H., Ikeguchi, M., Park, S.Y., Watashi, K.

(2024) Nat Commun 15: 9241-9241

• PubMed: 39455604 
• DOI: https://doi.org/10.1038/s41467-024-53533-6
• Primary Citation of Related Structures:  
  8XCD


• PubMed Abstract: 
  

  Macaque restricts hepatitis B virus (HBV) infection because its receptor homologue, NTCP (mNTCP), cannot bind preS1 on viral surface. To reveal how mNTCP loses the viral receptor function, we here solve the cryo-electron microscopy structure of mNTCP. Superposing on the human NTCP (hNTCP)-preS1 complex structure shows that Arg158 of mNTCP causes steric clash to prevent preS1 from embedding onto the bile acid tunnel of NTCP. Cell-based mutation analysis confirms that only Gly158 permitted preS1 binding, in contrast to robust bile acid transport among mutations. As the second determinant, Asn86 on the extracellular surface of mNTCP shows less capacity to restrain preS1 from dynamic fluctuation than Lys86 of hNTCP, resulting in unstable preS1 binding. Additionally, presence of long-chain conjugated-bile acids in the tunnel induces steric hindrance with preS1 through their tailed-chain. This study presents structural basis in which multiple sites in mNTCP constitute a molecular barrier to strictly restrict HBV.

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Organizational Affiliation: 
• Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
Graduate School of Science and Technology, Tokyo University of Science, Chiba, Japan.
Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan.
Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan.
Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
RIKEN SPring-8 Center, Hyogo, Japan.
Department of Infectious Disease Research, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan.
HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Kanagawa, Japan.
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan. [e-mail].
Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan. [e-mail].
Graduate School of Science and Technology, Tokyo University of Science, Chiba, Japan. [e-mail].
Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 90.14 kDa 
• Atom Count: 5,626 
• Modeled Residue Count: 727 
• Deposited Residue Count: 819 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 10 member a1	A	351	Macaca fascicularis	Mutation(s): 0  Gene Names: Slc10a1 Membrane Entity: Yes
UniProt
Find proteins for G7PAR4 (Macaca fascicularis) Explore G7PAR4  Go to UniProtKB:  G7PAR4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YN69083 Fab Heavy chain	B [auth H]	255	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
YN69083 Fab Light chain	C [auth L]	213	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TCH (Subject of Investigation/LOI)	D [auth A], E [auth A]	TAUROCHOLIC ACID C26 H45 N O7 S WBWWGRHZICKQGZ-HZAMXZRMSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Park, J.H., Ishimoto, N., Park, S.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references
• Version 1.2: 2024-11-27
  Changes: Data collection