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- PDB-8yy8: Fzd7 -Gs complex -

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Basic information

Entry
Database: PDB / ID: 8yy8
TitleFzd7 -Gs complex
Components
  • Frizzled-7
  • 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
  • Nb35
  • minGas
KeywordsMEMBRANE PROTEIN / GPCR / Class F / Frizzled / Fzd7 / Frizzled 7 / Fzd7-Gs complex
Function / homology
Function and homology information


negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / Wnt-protein binding / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / Wnt-protein binding / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / regulation of canonical Wnt signaling pathway / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of phosphorylation / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / positive regulation of JNK cascade / 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 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 / neuron differentiation / 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 / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / recycling endosome membrane / GPER1 signaling / 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) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / T cell differentiation in thymus / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / synapse / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Frizzled-7, cysteine-rich Wnt-binding domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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 beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Frizzled-7 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsChen, B. / Xu, L. / Han, G.W. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018YFA0507000 China
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structure of constitutively active human Frizzled 7 in complex with heterotrimeric G.
Authors: Lu Xu / Bo Chen / Hannes Schihada / Shane C Wright / Ainoleena Turku / Yiran Wu / Gye-Won Han / Maria Kowalski-Jahn / Pawel Kozielewicz / Carl-Fredrik Bowin / Xianjun Zhang / Chao Li / ...Authors: Lu Xu / Bo Chen / Hannes Schihada / Shane C Wright / Ainoleena Turku / Yiran Wu / Gye-Won Han / Maria Kowalski-Jahn / Pawel Kozielewicz / Carl-Fredrik Bowin / Xianjun Zhang / Chao Li / Michel Bouvier / Gunnar Schulte / Fei Xu /
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 24, 2024ID: 7EVW
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: minGas
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nb35
R: Frizzled-7


Theoretical massNumber of molelcules
Total (without water)158,9595
Polymers158,9595
Non-polymers00
Water0
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

#1: Protein minGas


Mass: 28907.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 10366.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P59768
#4: Protein Nb35


Mass: 16054.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein Frizzled-7 / / Fz-7 / hFz7 / FzE3


Mass: 66213.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75084

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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: human Frizzled 7 in complex with heterotrimeric Gs / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224750 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038852
ELECTRON MICROSCOPYf_angle_d0.5511981
ELECTRON MICROSCOPYf_dihedral_angle_d4.5561201
ELECTRON MICROSCOPYf_chiral_restr0.0441318
ELECTRON MICROSCOPYf_plane_restr0.0051529

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