+Open data
-Basic information
Entry | Database: PDB / ID: 8rqf | |||||||||||||||
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Title | Cryo-EM structure of human NTCP-Bulevirtide complex | |||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Hepatitis B/D virus receptor / bile salt transporter / drugs / inhibitor | |||||||||||||||
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) Lama glama (llama) hepatitis B virus genotype C | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
Authors | Liu, H. / Zakrzewicz, D. / Nosol, K. / Irobalieva, R.N. / Mukherjee, S. / Bang-Soerensen, R. / Goldmann, N. / Kunz, S. / Rossi, L. / Kossiakoff, A.A. ...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 support | Switzerland, Germany, United States, 4items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human NTCP-Bulevirtide complex Authors: 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. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rqf.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rqf.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 8rqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rqf_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8rqf_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8rqf_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 8rqf_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/8rqf ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rqf | HTTPS FTP |
-Related structure data
Related structure data | 19440MC 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
-Antibody , 3 types, 3 molecules HLK
#2: Antibody | Mass: 25197.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#3: Antibody | Mass: 23481.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#4: Antibody | Mass: 13118.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 38149.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC10A1, NTCP, GIG29 / Production host: Homo sapiens (human) / References: UniProt: Q14973 |
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#5: Protein/peptide | Mass: 5136.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) hepatitis B virus genotype C / References: UniProt: A0A515J2X9 |
-Non-polymers , 2 types, 2 molecules
#6: Chemical | ChemComp-BJU / Mass: 285.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H31NO3 / Feature type: SUBJECT OF INVESTIGATION |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-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: Structure of Bulevirtide-bound human NTCP in complex with Fab and nanobody Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.11 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128700 / Symmetry type: POINT |