7DW9 | pdb_00007dw9

Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein

• PDB DOI: https://doi.org/10.2210/pdb7DW9/pdb
• EM Map EMD-30877: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-01-15 Released: 2021-07-21 
• Deposition Author(s): Zhou, F., Jiang, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of ligand recognition and activation of human V2 vasopressin receptor.

Zhou, F., Ye, C., Ma, X., Yin, W., Croll, T.I., Zhou, Q., He, X., Zhang, X., Yang, D., Wang, P., Xu, H.E., Wang, M.W., Jiang, Y.

(2021) Cell Res 31: 929-931

• PubMed: 33742150 
• DOI: https://doi.org/10.1038/s41422-021-00480-2
• Primary Citation of Related Structures:  
  7DW9

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Organizational Affiliation: 
• The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
School of Pharmacy, Fudan University, Shanghai, 201203, China.
Cryo-EM Centre, Southern University of Science and Technology, Shenzhen, Guangdong, 515055, China.
Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK.
School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China.
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
Cryo-EM Centre, Southern University of Science and Technology, Shenzhen, Guangdong, 515055, China. [e-mail].
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 515055, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
School of Pharmacy, Fudan University, Shanghai, 201203, China. [e-mail].
School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A1B1C1D1E1F1G1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 204.9 kDa 
• Atom Count: 10,105 
• Modeled Residue Count: 1,284 
• Deposited Residue Count: 1,845 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vasopressin V2 receptor	A [auth R]	645	Homo sapiens	Mutation(s): 0  Gene Names: AVPR2, ADHR, DIR, DIR3, V2R Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens) Explore P30518  Go to UniProtKB:  P30518
PHAROS:  P30518 GTEx:  ENSG00000126895

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	B [auth A]	361	Homo sapiens	Mutation(s): 0  EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955
UniProt Groups	P63096P63092

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	371	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth Y]	71	Bos taurus	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody35	E [auth N]	140	synthetic construct	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	F [auth S]	247	synthetic construct	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
CYS-TYR-PHE-GLN-ASN-CYS-PRO-ARG-GLY-NH2	G [auth C]	10	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P01185 (Homo sapiens) Explore P01185  Go to UniProtKB:  P01185
PHAROS:  P01185 GTEx:  ENSG00000101200

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	H [auth R], I [auth R], J [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Zhou, F., Jiang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0507002
National Natural Science Foundation of China (NSFC)	China	31770796
National Natural Science Foundation of China (NSFC)	China	81872915
National Natural Science Foundation of China (NSFC)	China	31600606
National Natural Science Foundation of China (NSFC)	China	81773792
Wellcome Trust	European Union	209407/Z/17/Z

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary