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- PDB-9u40: Cryo-EM structure of peptide GPCR-Gq complex -

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Basic information

Entry
Database: PDB / ID: 9u40
TitleCryo-EM structure of peptide GPCR-Gq complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Arg-vasopressin
  • Nanobody 35
  • exo-alpha-sialidase,Vasopressin V1a receptor
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Vasopressin / GPCR / Complex / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V1B vasopressin receptor binding / : / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / V1A vasopressin receptor binding / negative regulation of female receptivity / cellular response to water deprivation / neurohypophyseal hormone activity / response to nerve growth factor / maternal aggressive behavior / negative regulation of transmission of nerve impulse ...V1B vasopressin receptor binding / : / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / V1A vasopressin receptor binding / negative regulation of female receptivity / cellular response to water deprivation / neurohypophyseal hormone activity / response to nerve growth factor / maternal aggressive behavior / negative regulation of transmission of nerve impulse / Organic anion transport by SLCO transporters / myotube differentiation / grooming behavior / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sperm ejaculation / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors / renal water absorption / vasopressin receptor activity / response to peptide / response to 2,3,7,8-tetrachlorodibenzodioxine / telencephalon development / positive regulation of prostaglandin biosynthetic process / vasoconstriction / maternal behavior / water transport / ganglioside catabolic process / neuropeptide hormone activity / oligosaccharide catabolic process / blood circulation / response to corticosterone / positive regulation of glutamate secretion / exo-alpha-sialidase / positive regulation of systemic arterial blood pressure / exo-alpha-sialidase activity / response to testosterone / peptide hormone binding / social behavior / response to electrical stimulus / response to salt stress / multicellular organismal response to stress / positive regulation of vasoconstriction / endocytic vesicle / positive regulation of heart rate / neuronal dense core vesicle / cellular response to hormone stimulus / transport across blood-brain barrier / BMAL1:CLOCK,NPAS2 activates circadian expression / secretory granule / locomotory behavior / protein kinase C binding / calcium-mediated signaling / response to nicotine / generation of precursor metabolites and energy / clathrin-coated endocytic vesicle membrane / hormone activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / cell-cell signaling / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / positive regulation of cell growth / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / Cargo recognition for clathrin-mediated endocytosis / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / Clathrin-mediated endocytosis / G-protein beta-subunit binding / extracellular vesicle / positive regulation of cytosolic calcium ion concentration / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / GTPase binding / Ca2+ pathway
Similarity search - Function
Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones signature. ...Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / BNR repeat-like domain / Vasopressin receptor / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily / 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 WD-40 repeat protein / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / Concanavalin A-like lectin/glucanase domain superfamily / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Vasopressin-neurophysin 2-copeptin / Vasopressin V1a 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 / exo-alpha-sialidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Homo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsLiu, S.H. / Zhang, Y.J. / Hua, T. / Liu, Z.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of peptide GPCR-Gq complex
Authors: Liu, S.H. / Zhang, Y.J. / Hua, T. / Liu, Z.J.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: exo-alpha-sialidase,Vasopressin V1a receptor
P: Arg-vasopressin
A: Guanine nucleotide-binding protein G(q) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanobody 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,1147
Polymers191,0896
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#3: Protein Guanine nucleotide-binding protein G(q) subunit alpha-1


Mass: 28084.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 41055.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768

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Protein / Protein/peptide / Antibody / Non-polymers , 4 types, 4 molecules RPN

#1: Protein exo-alpha-sialidase,Vasopressin V1a receptor / V1aR / AVPR V1a / Antidiuretic hormone receptor 1a / Vascular/hepatic-type arginine vasopressin receptor


Mass: 95943.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria), (gene. exp.) Homo sapiens (human)
Gene: nanH, AVPR1A, AVPR1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q59310, UniProt: P37288, exo-alpha-sialidase
#2: Protein/peptide Arg-vasopressin / Arginine-vasopressin


Mass: 1086.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01185
#6: Antibody Nanobody 35


Mass: 17057.271 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)
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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

ComponentName: V1aR with Gq / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313990 / Symmetry type: POINT
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048387
ELECTRON MICROSCOPYf_angle_d0.55111371
ELECTRON MICROSCOPYf_dihedral_angle_d4.0971135
ELECTRON MICROSCOPYf_chiral_restr0.0421270
ELECTRON MICROSCOPYf_plane_restr0.0051455

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