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- PDB-9epo: High resolution structure of FZD7 in inactive conformation -

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Basic information

Entry
Database: PDB / ID: 9epo
TitleHigh resolution structure of FZD7 in inactive conformation
ComponentsFrizzled-7
KeywordsMEMBRANE PROTEIN / GPCPR / Frizzled / FZD7
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 / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / 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 / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / canonical Wnt signaling pathway / positive regulation of phosphorylation / cellular response to retinoic acid / 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 / neuron differentiation / recycling endosome membrane / T cell differentiation in thymus / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / membrane / plasma membrane
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.
Similarity search - Domain/homology
PALMITIC ACID / CHOLESTEROL HEMISUCCINATE / Frizzled-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsBous, J. / Kinsolving, J. / Gratz, L. / Scharf, M.M. / Voss, J. / Selcuk, B. / Adebali, O. / Schulte, G.
Funding support Sweden, Germany, 7items
OrganizationGrant numberCountry
Other government2021-00430 (Karolinska Instutet) Sweden
Swedish Research Council2019-01190 Sweden
Other government20 1102 (Swedish Cancer Society) Sweden
Other government23 2825 (Swedish Cancer Society) Sweden
Other privateUPD2021-0029 (Wenner Gren Foundation) Sweden
German Research Foundation (DFG)504098926 Germany
German Research Foundation (DFG)520506488 Germany
CitationJournal: To Be Published
Title: high-resolution structural characterization of FZD7 unravels the importance of water network and cholesterol for class F GPCRs dynamic and activation
Authors: Bous, J. / Kinsolving, J. / Gratz, L. / Scharf, M.M. / Voss, J. / Selcuk, B. / Adebali, O. / Schulte, G.
History
DepositionMar 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frizzled-7
D: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3818
Polymers134,9222
Non-polymers2,4606
Water1,69394
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 Frizzled-7 / Fz-7 / hFz7 / FzE3


Mass: 67460.859 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: FZD7 anti-parallel Dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 134788 kDa/nm / Experimental value: NO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.01 Mtris hydrochlorideTRIS-HCL1
20.1 MSodium ChlorideNaCl1
30.0002 %cholesteryl hemisuccinate tris saltCHS1
40.002 %Lauryl Maltose Neopentyl GlycolLMNG1
50.0002 %glyco-diosgeninGDN1
SpecimenConc.: 3.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21081

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5particle selection
2EPUimage acquisition
4cryoSPARC4.4.0CTF correction
7Coot0.9model fitting
9cryoSPARC4.4.0initial Euler assignment
10cryoSPARC4.4.0final Euler assignment
11cryoSPARC4.4.0classification
12cryoSPARC4.4.03D reconstruction
13Rosettamodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7332734
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145595 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7evw

7evw
PDB Unreleased entry


Pdb chain-ID: R / Accession code: 7evw / Source name: PDB / Type: experimental model

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