7ZYI

Structure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody

• PDB DOI: https://doi.org/10.2210/pdb7ZYI/pdb
• EM Map EMD-15024: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-05-24 Released: 2022-07-13 
• Deposition Author(s): Liu, H., Irobalieva, R.N., Bang-Sorensen, R., Nosol, K., Mukherjee, S., Agrawal, P., Stieger, B., Kossiakoff, A.A., Locher, K.P.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of human NTCP reveals the basis of recognition and sodium-driven transport of bile salts into the liver.

Liu, H., Irobalieva, R.N., Bang-Sorensen, R., Nosol, K., Mukherjee, S., Agrawal, P., Stieger, B., Kossiakoff, A.A., Locher, K.P.

(2022) Cell Res 32: 773-776

• PubMed: 35726088 
• DOI: https://doi.org/10.1038/s41422-022-00680-4
• Primary Citation of Related Structures:  
  7ZYI

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 101.99 kDa 
• Atom Count: 6,641 
• Modelled Residue Count: 852 
• Deposited Residue Count: 922 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/bile acid cotransporter	A	349	Homo sapiens	Mutation(s): 0  Gene Names: SLC10A1, NTCP, GIG29 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q14973 (Homo sapiens) Explore Q14973  Go to UniProtKB:  Q14973
PHAROS:  Q14973 GTEx:  ENSG00000100652

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of Fab	B [auth H]	238	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of Fab	C [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	D [auth K]	120	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHO (Subject of Investigation/LOI)	F [auth A], G [auth A]	GLYCOCHENODEOXYCHOLIC ACID C26 H43 N O5 GHCZAUBVMUEKKP-GYPHWSFCSA-N
CLR	E [auth A], H [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NA	I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Liu, H., Irobalieva, R.N., Bang-Sorensen, R., Nosol, K., Mukherjee, S., Agrawal, P., Stieger, B., Kossiakoff, A.A., Locher, K.P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2022-07-20
  Changes: Data collection, Structure summary
• Version 1.2: 2022-08-10
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection