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- EMDB-37869: Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43 -

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Basic information

Entry
Database: EMDB / ID: EMD-37869
TitleCryo-EM structure of LGR4 in complex with Rspo1 and RNF43
Map data
Sample
  • Complex: LGR4 in complex with Rspo1 and RNF43
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: R-spondin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RNF43
Keywordscomplex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


metanephric glomerulus development / metanephric nephron tubule morphogenesis / Wnt receptor catabolic process / 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 ...metanephric glomerulus development / metanephric nephron tubule morphogenesis / Wnt receptor catabolic process / 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 / positive regulation of Wnt signaling pathway / hair follicle development / 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 / 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 / positive regulation of protein phosphorylation / 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. / Ring finger / Growth factor receptor cysteine-rich domain superfamily / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsChang Z / Lin C
Funding support1 items
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, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37869.png

Downloads & links

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Map

FileDownload / File: emd_37869.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.148
Minimum - Maximum-0.001709838 - 2.1238165
Average (Standard dev.)0.0011171817 (±0.023507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : LGR4 in complex with Rspo1 and RNF43

EntireName: LGR4 in complex with Rspo1 and RNF43
Components
  • Complex: LGR4 in complex with Rspo1 and RNF43
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: R-spondin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RNF43

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Supramolecule #1: LGR4 in complex with Rspo1 and RNF43

SupramoleculeName: LGR4 in complex with Rspo1 and RNF43 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Leucine-rich repeat-containing G-protein coupled receptor 4
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.869461 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAAPPLCA APCSCDGDRR VDCSGKGLTA VPEGLSAFTQ ALDISMNNIT QLPEDAFKNF PFLEELQLA GNDLSFIHPK ALSGLKELKV LTLQNNQLKT VPSEAIRGLS ALQSLRLDAN HITSVPEDSF EGLVQLRHLW L DDNSLTEV ...String:
MKTIIALSYI FCLVFADYKD DDDAAPPLCA APCSCDGDRR VDCSGKGLTA VPEGLSAFTQ ALDISMNNIT QLPEDAFKNF PFLEELQLA GNDLSFIHPK ALSGLKELKV LTLQNNQLKT VPSEAIRGLS ALQSLRLDAN HITSVPEDSF EGLVQLRHLW L DDNSLTEV PVHPLSNLPT LQALTLALNK ISSIPDFAFT NLSSLVVLHL HNNKIRSLSQ HCFDGLDNLE TLDLNYNNLG EF PQAIKAL PSLKELGFHS NSISVIPDGA FDGNPLLRTI HLYDNPLSFV GNSAFHNLSD LHSLVIRGAS MVQQFPNLTG TVH LESLTL TGTKISSIPN NLCQEQKMLR TLDLSYNNIR DLPSFNGCHA LEEISLQRNQ IYQIKEGTFQ GLISLRILDL SRNL IHEIH SRAFATLGPI TNLDVSFNEL TSFPTEGLNG LNQLKLVGNF KLKEALAAKD FVNLRSLSVP YAYQCCAFWG CDSYA NLNT EDNSLQDHSV AQEKGTADAA NVTSTLENEE HSQIIIHCTP STGAFKPCEY LLGSWMIRLT VWFIFLVALF FNLLVI LTT FASCTSLPSS KLFIGLISVS NLFMGIYTGI LTFLDAVSWG RFAEFGIWWE TGSGCKVAGF LAVFSSESAI FLLMLAT VE RSLSAKDIMK NGKSNHLKQF RVAALLAFLG ATVAGCFPLF HRGEYSASPL CLPFPTGETP SLGFTVTLVL LNSLAFLL M AVIYTKLYCN LEKEDLSENS QSSMIKHVAW LIFTNCIFFC PVAFFSFAPL ITAISISPEI MKSVTLIFFP LPACLNPVL YVFFNPKFKE DWKLLKRRVT KKSGSVSVSI SS

UniProtKB: Leucine-rich repeat-containing G-protein coupled receptor 4

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Macromolecule #2: R-spondin-1

MacromoleculeName: R-spondin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.313323 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
EGSQACAKGC ELCSEVNGCL KCSPKLFILL ERNDIRQVGV CLPSCPPGYF DARNPDMNKC IKCKIEHCEA CFSHNFCTKC KEGLYLHKG RCYPACPEGS SAANGTMECS SAAAHHHHHH HH

UniProtKB: R-spondin-1

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Macromolecule #3: E3 ubiquitin-protein ligase RNF43

MacromoleculeName: E3 ubiquitin-protein ligase RNF43 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.501211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
QKAIIRVIPL KMDPTGKLNL TLEGVFAGVA EITPAEGKLM QSHPLYLCNA SDDDNLEPGF ISIVKLESPR RAPRPCLSLA SKARMAGER GASAVLFDIT EDRAAAEQLQ QPLGLTWPVV LIWGNDAEKL MEFVYKNQKA HVRIELKEPP AWPDYDAAAH H HHHHHH

UniProtKB: E3 ubiquitin-protein ligase RNF43

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124586
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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