8HRX: Human NTCP-myr-preS1-YN9048Fab complex

Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex. Determined by electron microscopy at 2.89 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 2.89 Å
Organisms: Homo sapiens, Hepatitis B virus, Ondatra zibethicus
Chains: 4
Atoms: 6,013
Mol. weight: 94.67 kDa
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8HRX contains 22 α-helices and 44 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	22-43	22
α-helix	48-56	9
α-helix	59-83	25
α-helix	87-98	12
α-helix	100-101	2
α-helix	104-110	7
α-helix	116-142	27
α-helix	157-179	23
α-helix	181-183	3
α-helix	184-210	27
α-helix	211-213	3
α-helix	214-217	4
α-helix	220-243	24
α-helix	248-258	11
α-helix	264-273	10
α-helix	281-284	4
α-helix	285-310	26

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: 2 helices, 19 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	4
β-strand	45-51	7	4
β-strand	58-60	3	4
β-strand	69-71	3	3
β-strand	78-82	5	3
β-strand	92-99	8	4
β-strand	105-108	4	4
β-strand	112-116	5	4
α-helix	119-121	3
β-strand	125-129	5	5
β-strand	140-150	11	5
β-strand	156-158	3	6
β-strand	168-170	3	5
β-strand	174-175	2	5
β-strand	180-189	10	5
β-strand	200-204	5	6
β-strand	209-213	5	6
α-helix	216-218	3

Chain L: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	7
β-strand	10-12	3	8
β-strand	21-25	5	7
β-strand	33-39	7	8
β-strand	42-49	8	8
β-strand	53-54	2	8
β-strand	56	1	9
β-strand	58	1	9
β-strand	67	1	7
β-strand	70-73	4	7
β-strand	85-90	6	8
β-strand	98	1	8
β-strand	102-105	4	8
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	145-148	4	11
β-strand	159-161	3	10
β-strand	173-174	2	10
β-strand	177-182	6	10
β-strand	192-197	6	11
β-strand	205-209	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/bile acid cotransporter	A	protein	343	Homo sapiens	Q14973 (AlphaFold model)
PreS1 protein (Fragment)	B	protein	55	Hepatitis B virus	Q67926
Fab heavy chain from antibody IgG clone number YN9048	H	protein	246	Ondatra zibethicus
Fab light chain from antibody IgG clone number YN9048	L	protein	214	Ondatra zibethicus

Sequence of entity 1 (A), FASTA

>8HRX_1 Sodium/bile acid cotransporter (chains A)
MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKG
LAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSI
VMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKR
PQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVL
SALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLL
IAIFWCYEKFKTPKDKTKMIENLYFQGDYKDDDDKHHHHHHHH

Sequence of entity 2 (B), FASTA

>8HRX_2 PreS1 protein (Fragment) (chains B)
GTNLSVPNPLGFFPDHQLDPAFKANSENPDWDLNPHKDNWPDANKVGDYKDDDDK

Sequence of entity 3 (H), FASTA

>8HRX_3 Fab heavy chain from antibody IgG clone number YN9048 (chains H)
EVQLQESGPELVKPGDSVKMSCKASGYTFTDYYMDWVKQNHGKSLEWIGYIYPYNGGTNY
NQKFKGKATLTVDKSSSTAYMELHSLTSEDSAVYYCARRGRFPWLAYWGQGTLVTVSAAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPS

Sequence of entity 4 (L), FASTA

>8HRX_4 Fab light chain from antibody IgG clone number YN9048 (chains L)
DIVMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVRVLIYYTSRLHSGVPS
RFSGSGSGTDFSLTISNLEPEDIATYYCQQYSKFPWTFGGGTKLEIKRADAAPTVSIFPP
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…
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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