+Open data
-Basic information
Entry | Database: PDB / ID: 8hry | ||||||
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Title | Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / hepatitis / HBV | ||||||
Function / homology | Function and homology information bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid and bile salt transport / bile acid signaling pathway / Recycling of bile acids and salts / viral process / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus ...bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid and bile salt transport / bile acid signaling pathway / Recycling of bile acids and salts / viral process / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity / basolateral plasma membrane / response to ethanol / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hepatitis B virus Ondatra zibethicus (muskrat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å | ||||||
Authors | Asami, J. / Shimizu, T. / Ohto, U. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural basis of hepatitis B virus receptor binding. Authors: Jinta Asami / Jae-Hyun Park / Yayoi Nomura / Chisa Kobayashi / Junki Mifune / Naito Ishimoto / Tomoko Uemura / Kehong Liu / Yumi Sato / Zhikuan Zhang / Masamichi Muramatsu / Takaji Wakita / ...Authors: Jinta Asami / Jae-Hyun Park / Yayoi Nomura / Chisa Kobayashi / Junki Mifune / Naito Ishimoto / Tomoko Uemura / Kehong Liu / Yumi Sato / Zhikuan Zhang / Masamichi Muramatsu / Takaji Wakita / David Drew / So Iwata / Toshiyuki Shimizu / Koichi Watashi / Sam-Yong Park / Norimichi Nomura / Umeharu Ohto / 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. ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hry.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hry.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 8hry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hry_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8hry_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8hry_validation.xml.gz | 31 KB | Display | |
Data in CIF | 8hry_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hry ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hry | HTTPS FTP |
-Related structure data
Related structure data | 34982MC 8hrxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 38198.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTCP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14973 |
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#2: Protein | Mass: 6229.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: W5UNL7 |
#3: Antibody | Mass: 25306.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ondatra zibethicus (muskrat) / Production host: Mus musculus (house mouse) |
#4: Antibody | Mass: 23667.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ondatra zibethicus (muskrat) / Production host: Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NTCP-myr-preS1-YN9016Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 / Details: 25 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.01% GDN |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72000 / Symmetry type: POINT | ||||||||||||||||||||||||
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