9UVV: Vasopressin V2 receptor,Soluble cytochrome b562

Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan. Determined by electron microscopy at 3.02 Å resolution. Released 6 May 2026.

Method: Electron microscopy
Resolution: 3.02 Å
Organisms: Homo sapiens, Escherichia coli, Mus musculus
Chains: 3
Atoms: 6,121
Mol. weight: 111.53 kDa
Ligands: A1IT8
Released: 6 May 2026

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

Secondary structure: helices and β-sheets

9UVV contains 33 α-helices and 50 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 A: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	39-67	29
α-helix	73-88	16
α-helix	89-93	5
α-helix	94-102	9
α-helix	109-142	34
β-strand	152	1	1
β-strand	157	1	1
α-helix	158-170	13
α-helix	172-176	5
β-strand	178	1	2
β-strand	181	1	3
β-strand	191	1	3
β-strand	194	1	2
α-helix	204-210	7
α-helix	211-215	5
α-helix	216-255	40
α-helix	259-276	18
α-helix	292-316	25
α-helix	320-374	55
α-helix	385-404	20
α-helix	408-418	11

Chain H: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
α-helix	43-44	2
β-strand	45-52	8	10
β-strand	57-60	4	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
α-helix	99-100	2
β-strand	101	1	11
β-strand	104	1	11
β-strand	108-109	2	10
β-strand	113-117	5	10
α-helix	120-122	3
β-strand	123	1	12
α-helix	124-125	2
β-strand	126-130	5	13
α-helix	131-134	4
β-strand	141-151	11	13
β-strand	152	1	12
β-strand	157-160	4	14
α-helix	161-163	3
β-strand	170-171	2	13
α-helix	172-174	3
β-strand	175-177	3	13
β-strand	180-190	11	13
β-strand	200-205	6	14
α-helix	206-208	3
β-strand	210-215	6	14

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-25	7	4
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
α-helix	55	1
β-strand	62-66	5	4
β-strand	70-75	6	4
α-helix	80-82	3
β-strand	84-90	7	5
α-helix	96	1
β-strand	97-98	2	5
β-strand	102-106	5	5
β-strand	111	1	6
α-helix	112-113	2
β-strand	114-118	5	7
α-helix	122-126	5
β-strand	129-139	11	7
β-strand	140	1	6
β-strand	145-150	6	8
β-strand	153-155	3	8
β-strand	159-163	5	7
α-helix	164-167	4
β-strand	173-182	10	7
α-helix	183-187	5
β-strand	191-198	8	8
β-strand	201-210	10	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vasopressin V2 receptor,Soluble cytochrome b562	A	protein	486	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P30518 (AlphaFold model)
Light chain of anti-BRIL SRP2070 fab antibody	L	protein	235	Mus musculus
Heavy chain of anti-BRIL SRP2070 fab antibody	H	protein	290	Mus musculus

Sequence of entity 1 (A), FASTA

>9UVV_1 Vasopressin V2 receptor,Soluble cytochrome b562 (chains A)
MKTIIALSYIFCLVFADYKDDDDAENLYFQGMLMASTTSAVPGHPSLPSLPSNSSQERPL
DTRDPLLARAELALLSIVFVAVALSNGLVLAALARRGRRGHWAPIHVFIGHLCLADLAVA
LFQVLPQLAWKATDRFRGPDALCRAVKYLQMVGMYASSYMILAMTLDRHRAICRPMLAYR
HGSGAHWNRPVLVAWAFSLLLSLPQLFIFAQRNVEGGSGVTDCWACFAEPWGRRTYVTWI
ALMVFVAPTLGIAACQVLIFREIHASLADLEDNWETLNDNLKVIEKADNAAQVKDALTKM
RAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ
LKTTRNAYIQKYLAVAKTVRMTLVIVVVYVLCWAPFFLVQLWAAWDPEAPLEGAPFVLLM
LLASLNSCTNPWIYASFSSSVSSELRSLLCCARGRTPPSLGPQDESCTTASSSLAKDTSS
LEVLFQ

Sequence of entity 2 (L), FASTA

>9UVV_2 Light chain of anti-BRIL SRP2070 fab antibody (chains L)
MEAPAQLLFLLLLWLPSSRAMDIVLTQSPATLSVTPGDRVSLSCRASQSVSNYLHWYQQK
SHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPLTFG
AGTKLELRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGV
LNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>9UVV_3 Heavy chain of anti-BRIL SRP2070 fab antibody (chains H)
MEAPAQLLFLLLLWLPSSRAMQIQLQQSGPELVKPGASVKISCKASGYTFTDFYINWMKQ
RPGQGLEWIGWIFPGSGNTHYNEKFKGKATLIVDTSSSTAFMQLNSLTSEDSAVYFCTRP
VSYYYDFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLT
WNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR
GCLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

Ligands and cofactors

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

Primary citation

A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through <em>In Silico</em> Construct Optimization and de novo Protein Design. Kojima, A., Kawakami, K., Kobayashi, N. et al. bioRxiv (2026). DOI 10.64898/2026.04.02.716066

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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