9HAP: PDB entry 9HAP

Cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with tolvaptan. Determined by electron microscopy at 2.5 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 4
Atoms: 6,767
Mol. weight: 124.51 kDa
Ligands: A1IT8
Released: 4 Jun 2025

Explore 9HAP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HAP contains 37 α-helices and 57 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 H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	20-28	9	1
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-54	7	3
β-strand	61-63	3	3
β-strand	71-76	6	1
β-strand	81-87	7	1
α-helix	91-93	3
β-strand	95-102	8	3
α-helix	103-104	2
α-helix	108-111	4
β-strand	113	1	3
β-strand	118	1	1
β-strand	121-123	3	3
β-strand	124-125	2	2
α-helix	132-134	3
β-strand	135-138	4	4
β-strand	149-159	11	4
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	178-179	2	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	200-202	3
β-strand	208-214	7	5
β-strand	219-225	7	5

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	17-25	9	6
β-strand	33-39	7	7
β-strand	45-51	7	7
α-helix	54-56	3
β-strand	58-60	3	7
β-strand	68-73	6	6
β-strand	78-84	7	6
α-helix	88-90	3
β-strand	92-99	8	7
β-strand	108-110	3	7
β-strand	115-119	5	7

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	11-14	4	9
β-strand	20-26	7	8
β-strand	34-39	6	9
β-strand	46-50	5	9
β-strand	54-55	2	9
α-helix	56	1
β-strand	57	1	10
β-strand	59	1	10
β-strand	63-68	6	8
β-strand	71-76	6	8
β-strand	86-91	6	9
α-helix	95-97	3
β-strand	99-100	2	9
β-strand	104-108	5	9
β-strand	113	1	11
α-helix	114-115	2
β-strand	116-120	5	12
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	12
β-strand	142	1	11
β-strand	146-152	7	13
β-strand	155-156	2	13
β-strand	161-166	6	12
β-strand	175-184	10	12
α-helix	185-188	4
β-strand	193-200	8	13
β-strand	207-212	6	13

Chain R: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-66	29
α-helix	75-88	14
α-helix	89-93	5
α-helix	94-102	9
α-helix	109-142	34
α-helix	158-170	13
α-helix	174-177	4
β-strand	178	1	14
β-strand	194	1	14
α-helix	201-209	9
α-helix	210-215	6
α-helix	216-232	17
α-helix	265-296	32
α-helix	307-314	8
α-helix	317-328	12
α-helix	330-336	7
α-helix	501-522	22
α-helix	527-546	20
α-helix	563-584	22
α-helix	588-601	14
α-helix	602-606	5
α-helix	607-610	4
α-helix	611-614	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synthetic antibody, anti-BRIL Fab fragment, Heavy chain	H	protein	231	Homo sapiens
anti-BRIL Fab Nanobody	K	protein	141	Homo sapiens
Synthetic antibody, anti-BRIL Fab fragment, Light chain	L	protein	215	Homo sapiens
Vasopressin V2 receptor,Soluble cytochrome b562	R	protein	552	Homo sapiens, Escherichia coli	P30518 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9HAP_1 Synthetic antibody, anti-BRIL Fab fragment, Heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 2 (K), FASTA

>9HAP_2 anti-BRIL Fab Nanobody (chains K)
AQPAMAQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRS
GDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQG
TQVTVSSLEDYKDDKHHHHHH

Sequence of entity 3 (L), FASTA

>9HAP_3 Synthetic antibody, anti-BRIL Fab fragment, Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (R), FASTA

>9HAP_4 Vasopressin V2 receptor,Soluble cytochrome b562 (chains R)
MKTIIALSYIFCLVFADYKDDDDAWSHPQFEKGGGSGGGSGGGSWSHPQFEKLEVLQGPD
YKDDDDAASTTSAVPGHPSLPSLPSQSSQERPLDTRDPLLARAELALLSIVFVAVALSNG
LVLAALARRGRRGHWAPIHVFIGHLCLADLAVALFQVLPQLAWKATDRFRGPDALCRAVK
YLQMVGMYASSYMILAMTLDRHRAICRPMLAYRHGSGAHWNRPVLVAWAFSLLLSLPQLF
IFAQRNVEGGSGVTDCWACFAEPWGRRTYVTWIALMVFVAPTLGIAACQVLIFREIHASL
VPGPSERPGGRRRGRRTGSPGEGAHVSAAVAKTVRMTLVIVVVYVLCWAPFFLVQLWAAW
DPEAPLEGAPFVLLMLLASLNSCTNPWIYASFSSSVSSELRSLLCCARGRTPPSLGPQDE
SCTTASSSLAKDTSSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDA
QKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNA
YIQKYLRARSTL

Ligands and cofactors

ID	Name	Formula	Copies
A1IT8	(R)-Tolvaptan	C26 H25 Cl N2 O3	1

Primary citation

Inactive structures of the vasopressin V2 receptor reveal distinct binding modes for Tolvaptan and Mambaquaretin toxin. Fouillen, A., Bous, J., Couvineau, P. et al. Nat Commun (2025) 16:3899-3899. DOI 10.1038/s41467-025-59114-5 · PubMed

Other PDB entries of the same protein (UniProt P30518 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7DFC 2.49 Å, Crystal of Arrestin2-V2Rpp-3-Fab30 complex
9HB3 2.5 Å, cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with…
7DFA 2.54 Å, Crystal of Arrestin2-V2Rpp-4-Fab30 complex
4JQI 2.6 Å, Structure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide
7DW9 2.6 Å, Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein
9ZZO 2.6 Å, MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
7KH0 2.8 Å, Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs…
9WSV 2.8 Å, Cryo-EM structure of DAMGO-muOR-arrestin-1-Fab30 complex
9WSW 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 complex
9WSX 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex
9UVW 2.89 Å, Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody…

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