8HRY: Human NTCP-myr-preS1-YN9016Fab complex

Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex. Determined by electron microscopy at 3.11 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.11 Å
Organisms: Homo sapiens, Hepatitis B virus, Ondatra zibethicus
Chains: 4
Atoms: 6,016
Mol. weight: 93.4 kDa
Released: 17 Jan 2024

Explore 8HRY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HRY contains 25 α-helices and 43 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: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	22-42	21
α-helix	43-45	3
α-helix	48-56	9
α-helix	59-83	25
α-helix	87-98	12
α-helix	100-101	2
α-helix	104-111	8
α-helix	116-141	26
α-helix	157-179	23
α-helix	181-183	3
α-helix	184-210	27
α-helix	214-217	4
α-helix	220-243	24
α-helix	248-259	12
α-helix	263-273	11
α-helix	281-284	4
α-helix	285-311	27

Chain B: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	8	1	2
β-strand	18	1	2
β-strand	33	1	1

Chain H: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	10-12	3	4
β-strand	19-25	7	3
β-strand	34-39	6	5
β-strand	45-51	7	5
β-strand	58-60	3	5
β-strand	69-71	3	3
β-strand	78-82	5	3
α-helix	88-90	3
β-strand	93-98	6	5
β-strand	109-110	2	5
β-strand	114-115	2	5
β-strand	116-118	3	4
α-helix	121-123	3
β-strand	127-131	5	6
β-strand	142-152	11	6
β-strand	158-160	3	7
β-strand	171-172	2	6
α-helix	173-175	3
β-strand	176-177	2	6
β-strand	182-191	10	6
β-strand	202-206	5	7
β-strand	211-215	5	7

Chain L: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	10-12	3	9
β-strand	20-25	6	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	63-64	2	8
β-strand	67	1	8
β-strand	70-74	5	8
β-strand	85-90	6	9
β-strand	103-105	3	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	145-149	5	11
β-strand	154	1	11
β-strand	159-164	6	10
α-helix	165-166	2
β-strand	173-182	10	10
α-helix	186-188	3
β-strand	191-198	8	11
β-strand	201-210	10	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/bile acid cotransporter	A	protein	343	Homo sapiens	Q14973 (AlphaFold model)
Large S protein (Fragment)	B	protein	55	Hepatitis B virus	Q67926
Fab heavy chain from antibody IgG clone number YN9016	H	protein	236	Ondatra zibethicus
Fab light chain from antibody IgG clone number YN9016	L	protein	214	Ondatra zibethicus

Sequence of entity 1 (A), FASTA

>8HRY_1 Sodium/bile acid cotransporter (chains A)
MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKG
LAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSI
VMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKR
PQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVL
SALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLL
IAIFWCYEKFKTPKDKTKMIENLYFQGDYKDDDDKHHHHHHHH

Sequence of entity 2 (B), FASTA

>8HRY_2 Large S protein (Fragment) (chains B)
GTNLSVPNPLGFFPDHQLDPAFKANSENPDWDLNPHKDNWPDANKVGDYKDDDDK

Sequence of entity 3 (H), FASTA

>8HRY_3 Fab heavy chain from antibody IgG clone number YN9016 (chains H)
EVQLQESGAELVRPGTSVKMSCKAAGYTFTNYWIGWVKQRPGHGLEWIGDIYPGGGYTNY
NEKFKGKATLTADTSSSTAYMQLSSLTSEDSALYYCARMKINNQAWFAYWGQGTLVTVSA
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSS

Sequence of entity 4 (L), FASTA

>8HRY_4 Fab light chain from antibody IgG clone number YN9016 (chains L)
DIVMTQSPASLSASVGETVTITCRASENIYSYLTWYQQKQGKSPQLLVYNAKTLAEGVPS
RFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPFTFGTGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Structural basis of hepatitis B virus receptor binding. Asami, J., Park, J.H., Nomura, Y. et al. Nat Struct Mol Biol (2024) 31:447-454. DOI 10.1038/s41594-023-01191-5 · 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
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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