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- PDB-9qzq: CryoEM structure of nanodisc-reconstituted human NTCP in complex ... -

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Basic information

Entry
Database: PDB / ID: 9qzq
TitleCryoEM structure of nanodisc-reconstituted human NTCP in complex with grafted NTCP_Nb1 and NabFab
Components
  • Grafted Nanobody NTCP_Nb1
  • NabFab - Heavy Chain
  • NabFab - Light Chain
  • Sodium/bile acid cotransporter
KeywordsTRANSPORT PROTEIN / Solute Carrier Protein / Bile salt transporter / HBV/ HDV receptor / Sodium-coupled transport
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
Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily
Similarity search - Domain/homology
Hepatic sodium/bile acid cotransporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsYoon, D. / Nosol, K. / Rasouli, A. / Bang-Soerensen, R. / Irobalieva, R.N. / Liu, H. / Tajkhorshid, E. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Structure / Year: 2025
Title: Structure of nanobody-inhibited state of human bile salt transporter NTCP.
Authors: Daniel Yoon / Kamil Nosol / Ali Rasouli / Rose Bang-Sørensen / Rossitza N Irobalieva / Hongtao Liu / Emad Tajkhorshid / Kaspar P Locher /
Abstract: Sodium-taurocholate co-transporting polypeptide (NTCP) is a sodium-dependent transporter mediating the hepatic uptake of bile salts and serving as the receptor of hepatitis B and D viruses. While ...Sodium-taurocholate co-transporting polypeptide (NTCP) is a sodium-dependent transporter mediating the hepatic uptake of bile salts and serving as the receptor of hepatitis B and D viruses. While previous studies identified binding sites for sodium ions and substrates, the mechanism remains controversial. We here report a high-resolution structure of NTCP in a closed-tunnel conformation that does not feature substrate binding sites but reveals evidence of two bound sodium ions. To evaluate the functional relevance of this state and gain insight into the transport mechanism, we performed μs-scale molecular dynamics simulations of NTCP starting from distinct conformations and substrate and ion configurations. We observed that both the closed-tunnel and open-tunnel conformations are highly stable, but that the sodium ions and bile salt molecules can shift positions without substantial conformational changes. Our results suggest that the closed-tunnel conformation might represents an inactive state rather than an essential component of a productive transport cycle.
History
DepositionApr 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/bile acid cotransporter
H: NabFab - Heavy Chain
L: NabFab - Light Chain
N: Grafted Nanobody NTCP_Nb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3736
Polymers102,3274
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#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 / Production host: Homo sapiens (human) / References: UniProt: Q14973
#2: Antibody NabFab - Heavy Chain


Mass: 25684.463 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)
#3: Antibody NabFab - Light Chain


Mass: 23258.783 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 Grafted Nanobody NTCP_Nb1


Mass: 15233.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeEntity IDParent-IDSource
1Nanodisc-reconstituted structure of human NTCP in complex with grafted NTCP_Nb1 and NabFabCOMPLEX#1-#40RECOMBINANT
2Sodium-taurocholate co-transporting polypeptide (NTCP)ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3Nanobody-binding Fab fragment (NabFab)ORGANELLE OR CELLULAR COMPONENT#2-#31RECOMBINANT
4Grafted Nanobody NTCP_Nb1ORGANELLE OR CELLULAR COMPONENT#41RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Escherichia coli (E. coli)562
74Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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
Image recordingElectron dose: 54.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133506 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026630
ELECTRON MICROSCOPYf_angle_d0.59003
ELECTRON MICROSCOPYf_dihedral_angle_d3.398917
ELECTRON MICROSCOPYf_chiral_restr0.0411026
ELECTRON MICROSCOPYf_plane_restr0.0041124

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