9U81: Anti-BRIL Fab heavy chain

Cryo-EM structure of tolvaptan-bound human vasopressin V2 receptor complex with Fab. Determined by electron microscopy at 3.08 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.08 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 3
Atoms: 6,275
Mol. weight: 98.93 kDa
Ligands: A1ECF
Released: 10 Dec 2025

Explore 9U81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U81 contains 30 α-helices and 43 β-strands across 3 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, 20 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	35-42	8	3
β-strand	48-55	8	3
β-strand	60-63	4	3
α-helix	65-67	3
β-strand	72-76	5	1
β-strand	81-87	7	1
α-helix	91-93	3
β-strand	95-103	9	3
α-helix	108-111	4
β-strand	116	1	3
β-strand	121-123	3	3
β-strand	124-125	2	2
α-helix	132-133	2
β-strand	134-138	5	4
β-strand	149-159	11	4
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	204-206	3
β-strand	209-214	6	5
β-strand	219-224	6	5

Chain L: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
β-strand	11-14	4	7
β-strand	20-26	7	6
β-strand	34-39	6	7
β-strand	46-49	4	7
α-helix	54	1
β-strand	55	1	7
α-helix	56	1
β-strand	63-68	6	6
β-strand	71-76	6	6
β-strand	86-91	6	7
α-helix	95-97	3
β-strand	99-100	2	7
β-strand	104-108	5	7
α-helix	115	1
β-strand	116-120	5	8
α-helix	121-123	3
α-helix	124-129	6
β-strand	132-141	10	8
β-strand	148-152	5	9
β-strand	156-157	2	9
β-strand	161-165	5	8
β-strand	175-183	9	8
α-helix	185-189	5
β-strand	193-198	6	9
β-strand	207-212	6	9

Chain R: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	37-67	31
α-helix	73-96	24
α-helix	109-142	34
β-strand	153	1	10
β-strand	156	1	10
α-helix	158-170	13
α-helix	173-177	5
β-strand	181	1	11
β-strand	193	1	11
α-helix	206-210	5
α-helix	211-215	5
α-helix	216-1023	43
α-helix	1027-1045	19
α-helix	1048-1050	3
α-helix	1059-1062	4
α-helix	1065-1085	21
α-helix	1088-296	63
α-helix	307-327	21
α-helix	330-336	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-BRIL Fab heavy chain	H	protein	229	Homo sapiens
anti-BRIL Fab light chain	L	protein	216	Homo sapiens
Vasopressin V2 receptor,Soluble cytochrome b562	R	protein	460	Homo sapiens, Escherichia coli	P30518 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9U81_1 anti-BRIL Fab heavy chain (chains H)
ELSEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 2 (L), FASTA

>9U81_2 anti-BRIL Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIF
PPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>9U81_3 Vasopressin V2 receptor,Soluble cytochrome b562 (chains R)
MLMASTTSAVPGHPSLPSLPSNSSQERPLDTRDPLLARAELALLSIVFVAVALSNGLVLA
ALARRGRRGHWAPIHVFIGHLCLADLAVALFQVLPQLAWKATDRFRGPDALCRAVKYLQM
VGMYASSYMILAMTLDRHRAICRPMLAYRHGSGAHWNRPVLVAWAFSLLLSLPQLFIFAQ
RNVEGGSGVTDCWACFAEPWGRRTYVTWIALMVFVAPTLGIAACQVLIFREIHAARRQLA
DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDF
RHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLAAVAKTVR
MTLVIVVVYVLCWAPFFLVQLWAAWDPEAPLEGAPFVLLMLLASLNSCTNPWIYASFSSS
VSSELRSLLCCARGRTPPSLGPQDESCTTASSSLAKDTSS

Ligands and cofactors

ID	Name	Formula	Copies
A1ECF	Tolvaptan	C26 H25 Cl N2 O3	1

Primary citation

Structural insights into antagonist recognition by the vasopressin V2 receptor. Zhang, T., Liu, H., You, C. et al. Nat Commun (2025) 16:9734-9734. DOI 10.1038/s41467-025-64735-x · 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
9HAP 2.5 Å, Cryo-EM structure of inactive human arginine-vasopressin (AVP) V2 receptor (V2R) with…
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

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