7ZYI | pdb_00007zyi

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

---

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 Related Structures: 
  7ZYI

---

Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of Zürich, Zürich, Switzerland.
Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland. [e-mail].

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 
• Modeled 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.

---

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