9HB3: Mambaquaretin-1

cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with Mambaquaretin1 K39A (MQK39A). Determined by electron microscopy at 2.5 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Dendroaspis angusticeps, Homo sapiens
Chains: 5
Atoms: 7,139
Mol. weight: 130.39 kDa
Released: 4 Jun 2025

Explore 9HB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HB3 contains 42 α-helices and 59 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: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	31-35	5	1
β-strand	45	1	1
α-helix	48-55	8

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	2
β-strand	13-15	3	3
β-strand	19-28	10	2
β-strand	36-42	7	3
β-strand	48-54	7	3
β-strand	61-63	3	3
β-strand	71-76	6	2
β-strand	81-87	7	2
α-helix	91-93	3
β-strand	95-102	8	3
α-helix	108-111	4
β-strand	120-125	6	3
α-helix	128-130	3
β-strand	131	1	4
β-strand	134-136	3	5
α-helix	139-141	3
β-strand	149-151	3	6
β-strand	155-159	5	5
β-strand	160	1	4
β-strand	164-168	5	7
α-helix	169-171	3
β-strand	178-179	2	8
α-helix	180-182	3
β-strand	183-184	2	5
β-strand	190-193	4	5
β-strand	194-195	2	8
β-strand	197-199	3	6
α-helix	201-204	4
β-strand	208-214	7	7
α-helix	215-217	3
β-strand	219-225	7	7

Chain K: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
β-strand	33-39	7	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	108-110	3	11
β-strand	115-117	3	11
β-strand	118-119	2	10

Chain L: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	11-14	4	13
β-strand	20-26	7	12
β-strand	34-39	6	13
β-strand	46-50	5	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	86-91	6	13
α-helix	95-97	3
β-strand	99-100	2	13
β-strand	104-108	5	13
α-helix	114-115	2
β-strand	116-120	5	14
α-helix	121-123	3
α-helix	124-128	5
β-strand	131-141	11	14
β-strand	147-152	6	15
β-strand	155-156	2	15
α-helix	157	1
β-strand	161-165	5	14
α-helix	166-169	4
β-strand	175-184	10	14
α-helix	185-190	6
β-strand	193-199	7	15
β-strand	207-212	6	15

Chain R: 22 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-65	30
α-helix	66-68	3
α-helix	73-88	16
α-helix	89-93	5
α-helix	94-100	7
α-helix	110-140	31
α-helix	158-169	12
α-helix	174-177	4
β-strand	179	1	16
β-strand	193	1	16
α-helix	202-209	8
α-helix	210-215	6
α-helix	216-233	18
α-helix	265-296	32
α-helix	307-315	9
α-helix	317-328	12
α-helix	330-335	6
α-helix	501-523	23
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
Mambaquaretin-1	A	protein	57	Dendroaspis angusticeps	A0A1Z0YU59 (AlphaFold model)
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
arginine-vasopressin (AVP) V2 receptor (V2R)-BRIL,Vasopressin V2 receptor,Vasopressin V2 receptor	R	protein	552	Homo sapiens	P30518 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HB3_1 Mambaquaretin-1 (chains A)
RPSFCNLPVKPGPCNGFFSAFYYSQKTNKCHSFTYGGCAGNANRFSTIEKCRRTCVG

Sequence of entity 2 (H), FASTA

>9HB3_2 Synthetic antibody, anti-BRIL Fab fragment, Heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (K), FASTA

>9HB3_3 anti-BRIL Fab Nanobody (chains K)
AQPAMAQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRS
GDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQG
TQVTVSSLEDYKDDKHHHHHH

Sequence of entity 4 (L), FASTA

>9HB3_4 Synthetic antibody, anti-BRIL Fab fragment, Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (R), FASTA

>9HB3_5 arginine-vasopressin (AVP) V2 receptor (V2R)-BRIL,Vasopressin V2 receptor,Vasopressin V2 receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDAWSHPQFEKGGGSGGGSGGGSWSHPQFEKLEVLQGPD
YKDDDDAASTTSAVPGHPSLPSLPSQSSQERPLDTRDPLLARAELALLSIVFVAVALSNG
LVLAALARRGRRGHWAPIHVFIGHLCLADLAVALFQVLPQLAWKATDRFRGPDALCRAVK
YLQMVGMYASSYMILAMTLDRHRAICRPMLAYRHGSGAHWNRPVLVAWAFSLLLSLPQLF
IFAQRNVEGGSGVTDCWACFAEPWGRRTYVTWIALMVFVAPTLGIAACQVLIFREIHASL
VPGPSERPGGRRRGRRTGSPGEGAHVSAAVAKTVRMTLVIVVVYVLCWAPFFLVQLWAAW
DPEAPLEGAPFVLLMLLASLNSCTNPWIYASFSSSVSSELRSLLCCARGRTPPSLGPQDE
SCTTASSSLAKDTSSARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDA
QKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNA
YIQKYLRARSTL

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 A0A1Z0YU59 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M4V 1.06 Å, X-ray structure of the mambaquaretin-1, a selective antagonist of the vasopressin type 2…

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