7ZYI: Human sodium/bile acid cotransporter

Structure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody. Determined by electron microscopy at 2.88 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, Mus musculus, Lama glama
Chains: 4
Atoms: 6,641
Mol. weight: 101.99 kDa
Ligands: CHO, CLR
Released: 13 Jul 2022

Explore 7ZYI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZYI contains 32 α-helices and 61 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-42	21
α-helix	43-45	3
α-helix	48-56	9
α-helix	60-66	7
α-helix	67-71	5
α-helix	72-82	11
α-helix	87-96	10
α-helix	104-111	8
α-helix	116-141	26
β-strand	143	1	1
β-strand	146	1	1
α-helix	151-153	3
α-helix	156-179	24
α-helix	181-183	3
α-helix	184-212	29
α-helix	220-243	24
α-helix	248-259	12
α-helix	263-273	11
α-helix	280-282	3
α-helix	285-309	25

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	11-12	2	3
β-strand	17-25	9	2
β-strand	33-39	7	4
β-strand	45-52	8	4
β-strand	56-59	4	4
β-strand	67-72	6	2
β-strand	77-82A	7	2
α-helix	84-86	3
β-strand	88-95	8	4
α-helix	96-99	4
β-strand	100J-103	4	4
β-strand	107-109	3	4
β-strand	110-111	2	3
β-strand	120-124	5	5
α-helix	125-127	3
β-strand	136-137	2	6
β-strand	139-145	7	5
β-strand	151-154	4	7
α-helix	155-157	3
β-strand	159	1	7
β-strand	164-165	2	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-181	6	5
β-strand	183-184	2	6
α-helix	188-191	4
β-strand	195	1	8
β-strand	196-200	5	7
β-strand	205-207	3	7
β-strand	210	1	8

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	18-25	8	15
β-strand	33-39	7	16
β-strand	45-51	7	16
β-strand	57-59	3	16
β-strand	60	1	11
β-strand	68-72	5	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-95	8	16
β-strand	100D-103	4	16
β-strand	107-111	5	16

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	10
β-strand	97-98	2	10
β-strand	102-106	5	10
β-strand	110	1	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	144-150	7	14
β-strand	153-154	2	14
β-strand	159-163	5	13
α-helix	165-167	3
β-strand	173-182	10	13
α-helix	183-188	6
β-strand	191-198	8	14
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/bile acid cotransporter	A	protein	349	Homo sapiens	Q14973 (AlphaFold model)
heavy chain of Fab	H	protein	238	Mus musculus
light chain of Fab	L	protein	215	Mus musculus
Nanobody	K	protein	120	Lama glama

Sequence of entity 1 (A), FASTA

>7ZYI_1 Sodium/bile acid cotransporter (chains A)
MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKG
LAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSI
VMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKR
PQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVL
SALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLL
IAIFWCYEKFKTPKDKTKMIYTAATTEETIPGALGNGTYKGEDCSPCTA

Sequence of entity 2 (H), FASTA

>7ZYI_2 heavy chain of Fab (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSYSSIHWVRQAPGKGLEWVASISSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYMKQQSQMWYQRYWGFDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L), FASTA

>7ZYI_3 light chain of Fab (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYWSPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (K), FASTA

>7ZYI_4 Nanobody (chains K)
VQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYA
DSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
CHO	Glycochenodeoxycholic acid	C26 H43 N O5	2
CLR	Cholesterol	C27 H46 O	2

Water and common crystallization additives (NA) are not listed.

Primary citation

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. et al. Cell Res (2022) 32:773-776. DOI 10.1038/s41422-022-00680-4 · PubMed

Other PDB entries of the same protein (UniProt Q14973 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HRX 2.89 Å, Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex
8HRY 3.11 Å, Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex
9QZQ 3.11 Å, CryoEM structure of nanodisc-reconstituted human NTCP in complex with grafted NTCP_Nb1…
7FCI 3.3 Å, human NTCP in complex with YN69083 Fab
7PQQ 3.3 Å, Structure of thermostabilised human NTCP in complex with Megabody 91
7VAG 3.32 Å, Cryo-EM structure of human NTCP complexed with YN69202Fab in the presence of…
7WSI 3.32 Å, Cryo-EM structure of human NTCP (wild-type) complexed with YN69202Fab
7VAD 3.41 Å, Cryo-EM structure of human NTCP complexed with YN69202Fab
8RQF 3.41 Å, Cryo-EM structure of human NTCP-Bulevirtide complex
7PQG 3.7 Å, Structure of thermostabilised human NTCP in complex with nanobody 87

Browse structure collections

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