[English] 日本語
Yorodumi
- PDB-7kh0: Cryo-EM structure of the human arginine vasopressin AVP-vasopress... -

+
Open data


ID or keywords:

Loading...

-
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 / neurohypophyseal hormone activity / V1A vasopressin receptor binding / negative regulation of transmission of nerve impulse / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / negative regulation of female receptivity / Transport of organic anions ...V1B vasopressin receptor binding / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / neurohypophyseal hormone activity / V1A vasopressin receptor binding / negative regulation of transmission of nerve impulse / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / negative regulation of female receptivity / Transport of organic anions / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / water transport / hemostasis / positive regulation of prostaglandin biosynthetic process / telencephalon development / grooming behavior / multicellular organismal-level water homeostasis / negative regulation of adenylate cyclase activity / neuropeptide hormone activity / maternal behavior / vasoconstriction / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of glutamate secretion / GTP metabolic process / neuronal dense core vesicle / social behavior / positive regulation of systemic arterial blood pressure / response to testosterone / positive regulation of intracellular signal transduction / positive regulation of macroautophagy / endocytic vesicle / cellular response to hormone stimulus / Adenylate cyclase inhibitory pathway / activation of adenylate cyclase activity / positive regulation of vasoconstriction / positive regulation of cellular pH reduction / response to cytokine / BMAL1:CLOCK,NPAS2 activates circadian expression / secretory granule / generation of precursor metabolites and energy / locomotory behavior / response to nicotine / G protein-coupled receptor binding / clathrin-coated endocytic vesicle membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GDP binding / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Cargo recognition for clathrin-mediated endocytosis / sensory perception of taste / cell-cell signaling / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / GTPase binding / positive regulation of cytosolic calcium ion concentration / Ca2+ pathway / retina development in camera-type eye / midbody / positive regulation of cell growth / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / 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. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
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 1.0May 26, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 26, 2021Data content type: Primary map / Data content type: Primary map / Provider: 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
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.4May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22872
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

SoftwareName: PHENIX / Version: dev_3951: / Classification: refinement
EM softwareName: PHENIX / Category: model 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more