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- PDB-7zyi: Structure of the human sodium/bile acid cotransporter (NTCP) in c... -

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Basic information

Entry
Database: PDB / ID: 7zyi
TitleStructure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
Components
  • Nanobody
  • Sodium/bile acid cotransporter
  • heavy chain of Fab
  • light chain of Fab
KeywordsTRANSPORT PROTEIN / NTCP / membrane protein / transport / sodium/bile acid cotransporter
Function / homology
Function and homology information


bile acid:sodium symporter activity / bile acid transmembrane transporter activity / bile acid and bile salt transport / Recycling of bile acids and salts / response to nutrient levels / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity / response to ethanol / basolateral plasma membrane / plasma membrane
Similarity search - Function
Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Hepatic sodium/bile acid cotransporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLiu, H. / Irobalieva, R.N. / Bang-Sorensen, R. / Nosol, K. / Mukherjee, S. / Agrawal, P. / Stieger, B. / Kossiakoff, A.A. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Cell Res / Year: 2022
Title: Structure of human NTCP reveals the basis of recognition and sodium-driven transport of bile salts into the liver.
Authors: Hongtao Liu / Rossitza N Irobalieva / Rose Bang-Sørensen / Kamil Nosol / Somnath Mukherjee / Parth Agrawal / Bruno Stieger / Anthony A Kossiakoff / Kaspar P Locher /
History
DepositionMay 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Data collection / Structure summary / Category: audit_author / em_imaging
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 1.2Aug 10, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.4Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/bile acid cotransporter
H: heavy chain of Fab
L: light chain of Fab
K: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,98710
Polymers100,2694
Non-polymers1,7196
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium/bile acid cotransporter / Cell growth-inhibiting gene 29 protein / Na(+)/bile acid cotransporter / Na(+)/taurocholate ...Cell growth-inhibiting gene 29 protein / Na(+)/bile acid cotransporter / Na(+)/taurocholate transport protein / Sodium/taurocholate cotransporting polypeptide / Solute carrier family 10 member 1


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 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q14973

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Antibody , 3 types, 3 molecules HLK

#2: Antibody heavy chain of Fab


Mass: 25582.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody light chain of Fab


Mass: 23417.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody Nanobody


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)

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Non-polymers , 4 types, 7 molecules

#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13208

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2image acquisition
4GctfCTF correction
7Cootmodel fitting
10RELION4final Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161093 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036768
ELECTRON MICROSCOPYf_angle_d0.8659203
ELECTRON MICROSCOPYf_dihedral_angle_d7.314947
ELECTRON MICROSCOPYf_chiral_restr0.0841062
ELECTRON MICROSCOPYf_plane_restr0.0051133

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