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- PDB-7kh0: Cryo-EM structure of the human arginine vasopressin AVP-vasopress... -

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Basic information

Entry
Database: PDB / ID: 7kh0
TitleCryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs signaling complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Arg-vasopressin
  • Nanobody 35
  • Single Fab chain (scFv16)
  • Vasopressin V2 receptor
KeywordsSIGNALING PROTEIN / arginine vasopressin AVP / Gs / signaling complex
Function / homology
Function and homology information


V1B vasopressin receptor binding / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / Transport of organic anions / neurohypophyseal hormone activity / V1A vasopressin receptor binding / penile erection / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / regulation of renal sodium excretion ...V1B vasopressin receptor binding / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / Transport of organic anions / neurohypophyseal hormone activity / V1A vasopressin receptor binding / penile erection / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / regulation of renal sodium excretion / negative regulation of transmission of nerve impulse / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / negative regulation of female receptivity / protein kinase C signaling / hyperosmotic salinity response / water transport / hemostasis / telencephalon development / positive regulation of systemic arterial blood pressure / grooming behavior / positive regulation of prostaglandin biosynthetic process / negative regulation of adenylate cyclase activity / membrane organization / maternal behavior / neuropeptide hormone activity / vasoconstriction / renal water homeostasis / positive regulation of glutamate secretion / GTP metabolic process / positive regulation of intracellular signal transduction / G protein-coupled dopamine receptor signaling pathway / response to testosterone / negative regulation of release of cytochrome c from mitochondria / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / social behavior / positive regulation of macroautophagy / endocytic vesicle / Adenylate cyclase inhibitory pathway / positive regulation of vasoconstriction / cellular response to hormone stimulus / negative regulation of inflammatory response to antigenic stimulus / activation of adenylate cyclase activity / ERK1 and ERK2 cascade / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of cellular pH reduction / BMAL1:CLOCK,NPAS2 activates circadian gene expression / secretory granule / generation of precursor metabolites and energy / response to cytokine / locomotory behavior / G protein-coupled receptor binding / peptide binding / response to nicotine / clathrin-coated endocytic vesicle membrane / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Cargo recognition for clathrin-mediated endocytosis / GTPase binding
Similarity search - Function
Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Vasopressin V2 receptor / Vasopressin receptor / G-protein alpha subunit, group I ...Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Vasopressin V2 receptor / Vasopressin receptor / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Vasopressin-neurophysin 2-copeptin / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Vasopressin V2 receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, L. / Xu, J. / Gao, S. / Sun, D. / Liu, H. / Liu, Z. / Du, Y. / Zhang, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128641 United States
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structure of the AVP-vasopressin receptor 2-G signaling complex.
Authors: Lei Wang / Jun Xu / Sheng Cao / Dapeng Sun / Heng Liu / Qiuyuan Lu / Zheng Liu / Yang Du / Cheng Zhang /
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 29, 2023Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

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Assembly

Deposited unit
R: Vasopressin V2 receptor
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
A: Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion
L: Arg-vasopressin
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
S: Single Fab chain (scFv16)
N: Nanobody 35


Theoretical massNumber of molelcules
Total (without water)173,9417
Polymers173,9417
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16100 Å2
ΔGint-79 kcal/mol
Surface area54950 Å2

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BAG

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38613.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short fusion / G(i) alpha-3 / Adenylate cyclase-stimulating G alpha protein


Mass: 43298.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3, GNAS, GNAS1, GSP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08754, UniProt: P63092-2
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7432.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Antibody , 2 types, 2 molecules SN

#6: Antibody Single Fab chain (scFv16)


Mass: 26450.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#7: Antibody Nanobody 35


Mass: 14714.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Protein / Protein/peptide , 2 types, 2 molecules RL

#1: Protein Vasopressin V2 receptor / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor


Mass: 42346.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AVPR2, ADHR, DIR, DIR3, V2R / Production host: Homo sapiens (human) / References: UniProt: P30518
#4: Protein/peptide Arg-vasopressin / AVP-NPII


Mass: 1086.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AVP, ARVP, VP / Production host: Homo sapiens (human) / References: UniProt: P01185

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Vasopressin V2 receptor complex with Gs and AVPCOMPLEXall0RECOMBINANT
2Vasopressin V2 receptor, Arg-vasopressinCOMPLEX#1, #41RECOMBINANT
3Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Single Fab chain (scFv16)COMPLEX#2-#3, #5-#61RECOMBINANT
4Nanobody 35COMPLEX#71RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Spodoptera frugiperda (fall armyworm)7108
34Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3951: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 398038 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410213
ELECTRON MICROSCOPYf_angle_d0.56413846
ELECTRON MICROSCOPYf_dihedral_angle_d4.4661398
ELECTRON MICROSCOPYf_chiral_restr0.0431547
ELECTRON MICROSCOPYf_plane_restr0.0041769

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