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- EMDB-64380: Structure of the complex of LGR4_ECD with Norrin -

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Basic information

Entry
Database: EMDB / ID: EMD-64380
TitleStructure of the complex of LGR4_ECD with Norrin
Map data
Sample
  • Complex: Structure of the complex of LGR4_ECD with Norrin
    • Protein or peptide: MB52
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: Norrin,Immunoglobulin gamma-1 heavy chain
KeywordsLGR4 Norrin / MEMBRANE 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 / endothelial cell differentiation / negative regulation of toll-like receptor signaling pathway / microglial cell proliferation / dendritic spine development / establishment of blood-brain barrier / positive regulation of branching involved in ureteric bud morphogenesis / vacuole organization / protein targeting to lysosome / male genitalia development / microglia differentiation / bone remodeling / frizzled binding / digestive tract development / lens development in camera-type eye / negative regulation of cold-induced thermogenesis / exploration behavior / negative regulation of cytokine production / optic nerve development / immunoglobulin complex / smoothened signaling pathway / retinal ganglion cell axon guidance / bone mineralization / action potential / decidualization / blood vessel remodeling / hair follicle development / canonical Wnt signaling pathway / response to axon injury / 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 / : / spermatogenesis / angiogenesis / neuron apoptotic process / cellular response to hypoxia / adaptive immune response / 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 / extracellular region / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Leucine-rich repeat domain superfamily / Immunoglobulin V-set domain / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Norrin / Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Camelus ferus (Wild Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsGeng Y / Hu FZ / Qiao HR
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the complex of LGR4_ECD with Norrin
Authors: Geng Y / Hu FZ / Qiao HR
History
DepositionApr 25, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64380.png

Downloads & links

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Map

FileDownload / File: emd_64380.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 548.352 Å		1.07 Å/pix.
x 512 pix.
= 548.352 Å		1.07 Å/pix.
x 512 pix.
= 548.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.172
Minimum - Maximum-1.0869586 - 1.7673945
Average (Standard dev.)-0.00012791506 (±0.0074427007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 548.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64380_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64380_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64380_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the complex of LGR4_ECD with Norrin

EntireName: Structure of the complex of LGR4_ECD with Norrin
Components
  • Complex: Structure of the complex of LGR4_ECD with Norrin
    • Protein or peptide: MB52
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: Norrin,Immunoglobulin gamma-1 heavy chain

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Supramolecule #1: Structure of the complex of LGR4_ECD with Norrin

SupramoleculeName: Structure of the complex of LGR4_ECD with Norrin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MB52

MacromoleculeName: MB52 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus ferus (Wild Bactrian camel)
Molecular weightTheoretical: 59.266367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKIWLALAG LVLAFSASAQ VQLVESGGGL VQTKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTA GGGKNSCATF GAEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ A EILKLANQ ...String:
MKKIWLALAG LVLAFSASAQ VQLVESGGGL VQTKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTA GGGKNSCATF GAEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ A EILKLANQ VESDFNKLSS GHLKDYIGKC DASAISSANM TMQNQKNNWG NGCAGVEETQ SLLKTSAADF NNQTPQINQA QN LANTLIQ ELGNNPFRAS GGGSGGGGSG KLSDTYEQLS RLLTNDNGTN SKTSAQAINQ AVNNLNERAK TLAGGTTNSP AYQ ATLLAL RSVLGLWNSM GYAVICGGYT KSPGENNQKD FHYTDENGNG TTINCGGSTN SNGTHSYNGT NTLKADKNVS LSIE QYEKI HEAYQILSKA LKQAGLAPLN SKGEKLEAHV TTSKYGSLRL SCAASGYTYS PYCMGWFRQA PGKAREGVAT VDLDG STIY ADSVKGRFTI SQDNAKNTLY LQMNSLKPED TAMYYCASRT RAGVTCGLNW AIFSYWGQGT QVTVSSHHHH HH

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Macromolecule #2: Leucine-rich repeat-containing G-protein coupled receptor 4

MacromoleculeName: Leucine-rich repeat-containing G-protein coupled receptor 4
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.397508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFAAPPL CAAPCSCDGD RRVDCSGKGL TAVPEGLSAF TQALDISMNN ITQLPEDAFK NFPFLEELQL AGNDLSFIH PKALSGLKEL KVLTLQNNQL KTVPSEAIRG LSALQSLRLD ANHITSVPED SFEGLVQLRH LWLDDNSLTE V PVHPLSNL ...String:
MKTIIALSYI FCLVFAAPPL CAAPCSCDGD RRVDCSGKGL TAVPEGLSAF TQALDISMNN ITQLPEDAFK NFPFLEELQL AGNDLSFIH PKALSGLKEL KVLTLQNNQL KTVPSEAIRG LSALQSLRLD ANHITSVPED SFEGLVQLRH LWLDDNSLTE V PVHPLSNL PTLQALTLAL NKISSIPDFA FTNLSSLVVL HLHNNKIRSL SQHCFDGLDN LETLDLNYNN LGEFPQAIKA LP SLKELGF HSNSISVIPD GAFDGNPLLR TIHLYDNPLS FVGNSAFHNL SDLHSLVIRG ASMVQQFPNL TGTVHLESLT LTG TKISSI PNNLCQEQKM LRTLDLSYNN IRDLPSFNGC HALEEISLQR NQIYQIKEGT FQGLISLRIL DLSRNLIHEI HSRA FATLG PITNLDVSFN ELTSFPTEGL NGLNQLKLVG NFKLKEALAA KDFVNLRSLS VPYAYQCCAF WGCDSYANLN TEDNS LQDH SVAQEKGTAD AANVTSTLEN EEHSQIIIHC TPSTGAFKPC EYLLGSWMIR LTVWFIFLVA LFFNLLVILT TFASCT SLP SSKLFIGLIS VSNLFMGIYT GILTFLDAVS WGRFAEFGIW WETGSGCKVA GFLAVFSSES AIFLLMLATV ERSLSAK DI MKNGKSNHLK QFRVAALLAF LGATVAGCFP LFHRGEYSAS PLCLPFPTGE TPSLGFTVTL VLLNSLAFLL MAVIYTKL Y CNLEKEDLSE NSQSSMIKHV AWLIFTNCIF FCPVAFFSFA PLITAISISP EIMKSVTLIF FPLPACLNPV LYVFFNPKF KEDWKLLKRR VTKKSGSVSV SISSQGGCLE QDFYYDCGMY SHLQGNLTVC DCCESFLLTK PVSCKHLIKS HSCPALAVAS CQRPEGYWS DCGTQSAHSD YADEEDSFVS DSSDQVQACG RACFYQSRGF PLVRYAYNLP RVKDAAADYK DDDDK

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

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Macromolecule #3: Norrin,Immunoglobulin gamma-1 heavy chain

MacromoleculeName: Norrin,Immunoglobulin gamma-1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.313438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAKT DSSFIMDSDP RRCMRHHYVD SISHPLYKCS SKMVLLARCE GHCSQASRS EPLVSFSTVL KQPFRSSCHC CRPQTSKLKA LRLRCSGGMR LTATYRYILS CHCEECNSGG SGGSGGLEVL F QGPGGSGG ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAKT DSSFIMDSDP RRCMRHHYVD SISHPLYKCS SKMVLLARCE GHCSQASRS EPLVSFSTVL KQPFRSSCHC CRPQTSKLKA LRLRCSGGMR LTATYRYILS CHCEECNSGG SGGSGGLEVL F QGPGGSGG SGGKSCDKTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HN AKTKPRE EQYNSTYRVV SVLTVLHQDW LNGKEYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP SRDELTKNQV SLT CLVKGF YPSDIAVEWE SNGQPENNYK ATPPVLDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPG KDYKD DDDK

UniProtKB: Norrin, Immunoglobulin gamma-1 heavy chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1196610
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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