8RQF: Human NTCP-Bulevirtide complex

Cryo-EM structure of human NTCP-Bulevirtide complex. Determined by electron microscopy at 3.41 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organisms: Homo sapiens, Lama glama, hepatitis B virus genotype C
Chains: 5
Atoms: 6,950
Mol. weight: 105.37 kDa
Ligands: BJU
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8RQF contains 27 α-helices and 62 β-strands across 5 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	14-15	2
α-helix	22-42	21
α-helix	48-56	9
α-helix	60-82	23
α-helix	87-97	11
α-helix	105-110	6
α-helix	116-128	13
α-helix	130-141	12
α-helix	156-179	24
α-helix	181-183	3
α-helix	184-210	27
α-helix	211-216	6
α-helix	220-243	24
α-helix	250-259	10
α-helix	264-273	10
α-helix	276-279	4
α-helix	280-284	5
α-helix	285-310	26

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	19
β-strand	18	1	19

Chain H: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-7	2	2
β-strand	11-12	2	3
β-strand	18-22	5	2
β-strand	25	1	1
β-strand	34-39	6	4
β-strand	45-52	8	4
β-strand	56-59	4	4
β-strand	67-72	6	2
β-strand	77-82	6	2
α-helix	84-86	3
β-strand	88-93	6	4
β-strand	97-98	2	5
β-strand	100C-100D	2	5
β-strand	103	1	4
β-strand	107-109	3	4
β-strand	110-111	2	3
β-strand	120-123	4	6
α-helix	125-127	3
β-strand	136-137	2	7
β-strand	140-145	6	6
β-strand	151-154	4	8
α-helix	155-157	3
β-strand	159	1	8
β-strand	164-165	2	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-181	6	6
β-strand	183-184	2	7
α-helix	188-191	4
β-strand	195	1	9
β-strand	196-200	5	8
β-strand	205-207	3	8
β-strand	210	1	9

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	11-12	2	17
β-strand	18-22	5	16
β-strand	33-39	7	18
β-strand	45-51	7	18
β-strand	59	1	18
β-strand	68-72	5	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	18
β-strand	100D-103	4	18
β-strand	107-109	3	18
β-strand	110-111	2	17

Chain L: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	10
β-strand	12	1	11
β-strand	19-24	6	12
β-strand	25	1	10
β-strand	35-38	4	13
β-strand	45-48	4	13
β-strand	62-67	6	12
β-strand	70-75	6	12
β-strand	85-88	4	13
β-strand	102-103	2	13
β-strand	105	1	11
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-127	6
β-strand	130-139	10	14
β-strand	145-150	6	15
β-strand	153-154	2	15
β-strand	159-163	5	14
β-strand	173-181	9	14
α-helix	183-188	6
β-strand	191-197	7	15
β-strand	205-210	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/bile acid cotransporter	A	protein	349	Homo sapiens	Q14973 (AlphaFold model)
Heavy chain of Fab3	H	protein	235	Homo sapiens
Light chain of Fab3	L	protein	215	Homo sapiens
Fab-specific nanobody	K	protein	120	Lama glama
Polymerase	B	protein	46	hepatitis B virus genotype C	Q76R62

Sequence of entity 1 (A), FASTA

>8RQF_1 Sodium/bile acid cotransporter (chains A)
MEAHNASAPFNFTLPPNFGKRPTDLALSVILVFMLFFIMLSLGCTMEFSKIKAHLWKPKG
LAIALVAQYGIMPLTAFVLGKVFRLKNIEALAILVCGCSPGGNLSNVFSLAMKGDMNLSI
VMTTCSTFCALGMMPLLLYIYSRGIYDGDLKDKVPYKGIVISLVLVLIPCTIGIVLKSKR
PQYMRYVIKGGMIIILLCSVAVTVLSAINVGKSIMFAMTPLLIATSSLMPFIGFLLGYVL
SALFCLNGRCRRTVSMETGCQNVQLCSTILNVAFPPEVIGPLFFFPLLYMIFQLGEGLLL
IAIFWCYEKFKTPKDKTKMIYTAATTEETIPGALGNGTYKGEDCSPCTA

Sequence of entity 2 (H), FASTA

>8RQF_2 Heavy chain of Fab3 (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSSSYIHWVRQAPGKGLEWVASISPYYSY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYQYDYYYSYYAGLDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L), FASTA

>8RQF_3 Light chain of Fab3 (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYRYSLITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (K), FASTA

>8RQF_4 Fab-specific nanobody (chains K)
VQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYA
DSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS

Sequence of entity 5 (B), FASTA

>8RQF_5 Polymerase (chains B)
TNLSVPNPLGFFPDHQLDPAFGANSNNPDWDFNPNKDHWPEANKVG

Ligands and cofactors

ID	Name	Formula	Copies
BJU	N-tetradecanoylglycine	C16 H31 N O3	1

Primary citation

Structure of antiviral drug bulevirtide bound to hepatitis B and D virus receptor protein NTCP. Liu, H., Zakrzewicz, D., Nosol, K. et al. Nat Commun (2024) 15:2476-2476. DOI 10.1038/s41467-024-46706-w · 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
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
7PQG 3.7 Å, Structure of thermostabilised human NTCP in complex with nanobody 87

Browse structure collections

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