7DW9

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00480-2
Primary Citation of Related Structures:
7DW9

Organizational Affiliation

The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30518
Sequence Annotations Expand
Reference Sequence

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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 P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63096P63092
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody35	E [auth N]	140	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	F [auth S]	247	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain H [auth R] SDF format, chain I [auth R] SDF format, chain J [auth R] MOL2 format, chain H [auth R] MOL2 format, chain I [auth R] MOL2 format, chain J [auth R] mmCIF format, chain H [auth R] mmCIF format, chain I [auth R] mmCIF format, chain J [auth R]	H [auth R], I [auth R], J [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Interactions & Density Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Zhou, F.

Jiang, Y.

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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7DW9

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)