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- EMDB-37876: Cryo-EM structure of LGR4 in complex with Norrin -

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Basic information

Entry
Database: EMDB / ID: EMD-37876
TitleCryo-EM structure of LGR4 in complex with Norrin
Map data
Sample
  • Complex: LGR4 in complex with Norrin
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: Norrin
Keywordscomplex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / metanephric glomerulus development / metanephric nephron tubule morphogenesis / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / epithelial cell proliferation involved in renal tubule morphogenesis ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / metanephric glomerulus development / metanephric nephron tubule morphogenesis / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / ubiquitin-dependent endocytosis / intestinal stem cell homeostasis / glycine metabolic process / retina layer formation / retinal pigment epithelium development / establishment of blood-retinal barrier / negative regulation of toll-like receptor signaling pathway / microglial cell proliferation / dendritic spine development / endothelial cell differentiation / establishment of blood-brain barrier / positive regulation of branching involved in ureteric bud morphogenesis / vacuole organization / male genitalia development / protein targeting to lysosome / microglia differentiation / bone remodeling / frizzled binding / digestive tract development / negative regulation of cold-induced thermogenesis / lens development in camera-type eye / exploration behavior / negative regulation of cytokine production / optic nerve development / retinal ganglion cell axon guidance / smoothened signaling pathway / bone mineralization / action potential / decidualization / blood vessel remodeling / hair follicle development / response to axon injury / canonical Wnt signaling pathway / tricarboxylic acid cycle / visual perception / glutathione metabolic process / Regulation of FZD by ubiquitination / transforming growth factor beta receptor signaling pathway / cytokine activity / circadian regulation of gene expression / G protein-coupled receptor activity / Wnt signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / nervous system development / mitotic cell cycle / : / neuron apoptotic process / angiogenesis / spermatogenesis / cellular response to hypoxia / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / inflammatory response / innate immune response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / Glycoprotein hormone receptor family / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / Glycoprotein hormone receptor family / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Cystine-knot cytokine / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Norrin / Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsLin C / Chang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of LGR4 in complex with Norrin
Authors: Lin C / Chang Z
History
DepositionOct 24, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37876.png

Downloads & links

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Map

FileDownload / File: emd_37876.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. 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: 0.283
Minimum - Maximum-0.5625695 - 2.615245
Average (Standard dev.)0.0041726395 (±0.027450975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 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 Norrin

EntireName: LGR4 in complex with Norrin
Components
  • Complex: LGR4 in complex with Norrin
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: Norrin

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Supramolecule #1: LGR4 in complex with Norrin

SupramoleculeName: LGR4 in complex with Norrin / 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: Norrin

MacromoleculeName: Norrin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.794806 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
IMDSDPRRCM RHHYVDSISH PLYKCSSKMV LLARCEGHCS QASRSEPLVS FSTVLKQPFR SSCHCCRPQT SKLKALRLRC SGGMRLTAT YRYILSCHCE ECNS

UniProtKB: Norrin

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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: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 584272
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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