7VAG: Human NTCP

Cryo-EM structure of human NTCP complexed with YN69202Fab in the presence of myristoylated preS1 peptide. Determined by electron microscopy at 3.32 Å resolution. Released 25 May 2022.

Method: Electron microscopy
Resolution: 3.32 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,697
Mol. weight: 89.04 kDa
Released: 25 May 2022

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

Secondary structure: helices and β-sheets

7VAG contains 26 α-helices and 46 β-strands across 3 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, 0 β-strands

Element	Residues	Length
α-helix	16-20	5
α-helix	22-44	23
α-helix	48-56	9
α-helix	59-66	8
α-helix	67-71	5
α-helix	72-82	11
α-helix	87-98	12
α-helix	100-101	2
α-helix	103-112	10
α-helix	116-141	26
α-helix	157-179	23
α-helix	184-208	25
α-helix	215-217	3
α-helix	220-243	24
α-helix	250-259	10
α-helix	264-273	10
α-helix	281-283	3
α-helix	285-309	25

Chain H: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5-6	2	2
β-strand	10-12	3	3
β-strand	19-23	5	2
α-helix	29-31	3
β-strand	33-39	7	4
β-strand	45-52	8	4
β-strand	57-60	4	4
α-helix	63-65	3
β-strand	69-73	5	2
β-strand	78-82	5	2
α-helix	88-90	3
β-strand	93-101	9	4
β-strand	105-111	7	4
β-strand	112	1	1
β-strand	115-116	2	4
β-strand	117-119	3	3
β-strand	130-132	3	5
β-strand	143-149	7	5
β-strand	159-161	3	6
β-strand	171-177	7	5
β-strand	184-192	9	5
β-strand	202-206	5	6
β-strand	207	1	7
β-strand	212	1	7
β-strand	215-217	3	6

Chain L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	8
β-strand	11-12	2	9
β-strand	21-23	3	8
β-strand	40-44	5	10
β-strand	51-55	5	10
β-strand	59-60	2	10
α-helix	61	1
β-strand	69-73	5	8
β-strand	76-80	5	8
α-helix	86-88	3
β-strand	91-92	2	10
β-strand	95	1	10
β-strand	96	1	11
β-strand	102	1	11
β-strand	107-108	2	10
β-strand	109-110	2	9
β-strand	119	1	12
β-strand	122-123	2	13
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	13
β-strand	150-155	6	14
β-strand	158-159	2	14
β-strand	164-168	5	13
β-strand	178-187	10	13
β-strand	198-202	5	14
α-helix	209	1
β-strand	210-212	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/bile acid cotransporter	A	protein	343	Homo sapiens	Q14973 (AlphaFold model)
Fab heavy chain from antibody IgG clone number YN69202	H	protein	249	Mus musculus
Fab light chain from antibody IgG clone number YN69202	L	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>7VAG_1 Sodium/bile acid cotransporter (chains A)
MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKG
LAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSI
VMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKR
PQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVL
SALFCLNGRCRRTVSMETGCANVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLL
IAIFWCYEKFKTPKDKTKMIENLYFQGDYKDDDDKHHHHHHHH

Sequence of entity 2 (H), FASTA

>7VAG_2 Fab heavy chain from antibody IgG clone number YN69202 (chains H)
EVQLQQSGPELVKPGASVKMSCKASGYTFTSYIIHWVKQKPGQGLEWIGYINPYNDGTKY
NEKFKGKGTLTSDKSSSTAYMELSSLTSEDSAVYYCARSYYDGIPHYFDYWGQGTTLTVS
SAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQS
GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCP
APNLEGGPS

Sequence of entity 3 (L), FASTA

>7VAG_3 Fab light chain from antibody IgG clone number YN69202 (chains L)
DIVMTQSPSSLAVSAGEKVTMSCKSSQSLFNSRTRRNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYYLLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Structure of the bile acid transporter and HBV receptor NTCP. Asami, J., Kimura, K.T., Fujita-Fujiharu, Y. et al. Nature (2022) 606:1021-1026. DOI 10.1038/s41586-022-04845-4 · PubMed

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

7ZYI 2.88 Å, Structure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and…
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
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

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