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- PDB-8wvu: Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43 -

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Basic information

Entry
Database: PDB / ID: 8wvu
TitleCryo-EM structure of LGR4 in complex with Rspo1 and RNF43
Components
  • E3 ubiquitin-protein ligase RNF43
  • Leucine-rich repeat-containing G-protein coupled receptor 4
  • R-spondin-1
KeywordsSTRUCTURAL PROTEIN / complex
Function / homology
Function and homology information


Wnt receptor catabolic process / metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / Signaling by RNF43 mutants / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis ...Wnt receptor catabolic process / metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / Signaling by RNF43 mutants / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling / frizzled binding / digestive tract development / negative regulation of cold-induced thermogenesis / negative regulation of cytokine production / bone mineralization / negative regulation of Wnt signaling pathway / hair follicle development / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / stem cell proliferation / circadian regulation of gene expression / G protein-coupled receptor binding / G protein-coupled receptor activity / RING-type E3 ubiquitin transferase / Wnt signaling pathway / positive regulation of protein phosphorylation / ubiquitin-protein transferase activity / osteoblast differentiation / ubiquitin protein ligase activity / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / nuclear envelope / heparin binding / ubiquitin-dependent protein catabolic process / spermatogenesis / protein ubiquitination / signaling receptor binding / innate immune response / endoplasmic reticulum membrane / extracellular space / extracellular region / zinc ion binding / nucleus / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / : / Glycoprotein hormone receptor family / Ring finger domain / Leucine rich repeat N-terminal domain ...E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / : / Glycoprotein hormone receptor family / Ring finger domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Furin-like repeat / Furin-like repeats / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
R-spondin-1 / E3 ubiquitin-protein ligase RNF43 / Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsChang, Z. / Lin, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43
Authors: Lin, C. / Chang, Z.
History
DepositionOct 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat-containing G-protein coupled receptor 4
B: R-spondin-1
C: E3 ubiquitin-protein ligase RNF43


Theoretical massNumber of molelcules
Total (without water)123,6843
Polymers123,6843
Non-polymers00
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

#1: Protein Leucine-rich repeat-containing G-protein coupled receptor 4


Mass: 91869.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXB1
#2: Protein R-spondin-1 / Roof plate-specific spondin-1 / hRspo1


Mass: 13313.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSPO1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2MKA7
#3: Protein E3 ubiquitin-protein ligase RNF43


Mass: 18501.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF43 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q68DV7
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: LGR4 in complex with Rspo1 and RNF43 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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: PROPANE

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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 defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 63 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124586 / Symmetry type: POINT

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