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- EMDB-62340: Structure of the complex of LGR4 with Norrin (2:2) -

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Basic information

Entry
Database: EMDB / ID: EMD-62340
TitleStructure of the complex of LGR4 with Norrin (2:2)
Map data
Sample
  • Complex: Structure of the complex of LGR4 with Norrin (2:2)
    • 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


Norrin signaling pathway / extracellular matrix-cell signaling / metanephric glomerulus development / metanephric nephron tubule morphogenesis / protein-hormone receptor activity / negative regulation of toll-like receptor signaling pathway / vacuole organization / positive regulation of branching involved in ureteric bud morphogenesis / bone remodeling / frizzled binding ...Norrin signaling pathway / extracellular matrix-cell signaling / metanephric glomerulus development / metanephric nephron tubule morphogenesis / protein-hormone receptor activity / negative regulation of toll-like receptor signaling pathway / vacuole organization / positive regulation of branching involved in ureteric bud morphogenesis / bone remodeling / frizzled binding / negative regulation of cytokine production / negative regulation of cold-induced thermogenesis / bone mineralization / decidualization / immunoglobulin complex / visual perception / Regulation of FZD by ubiquitination / cytokine activity / circadian regulation of gene expression / Wnt signaling pathway / osteoblast differentiation / G protein-coupled receptor activity / positive regulation of canonical Wnt signaling pathway / transmembrane signaling receptor activity / nervous system development / spermatogenesis / adaptive immune response / innate immune response / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / : / 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 / 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 / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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 dromedarius (Arabian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsYong G / 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 with Norrin (2:2)
Authors: Yong G / Hu FZ / Qiao HR
History
DepositionNov 10, 2024-
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_62340.png

Downloads & links

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Map

FileDownload / File: emd_62340.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: 0.0853
Minimum - Maximum-0.20484884 - 0.4735509
Average (Standard dev.)-0.00012820569 (±0.0069269603)
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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Half map: #2

Fileemd_62340_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62340_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the complex of LGR4 with Norrin (2:2)

EntireName: Structure of the complex of LGR4 with Norrin (2:2)
Components
  • Complex: Structure of the complex of LGR4 with Norrin (2:2)
    • 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 with Norrin (2:2)

SupramoleculeName: Structure of the complex of LGR4 with Norrin (2:2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MB52

MacromoleculeName: MB52 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Camelus dromedarius (Arabian 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: Norrin,Immunoglobulin gamma-1 heavy chain

MacromoleculeName: Norrin,Immunoglobulin gamma-1 heavy chain / type: protein_or_peptide / ID: 2 / 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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Macromolecule #3: Leucine-rich repeat-containing G-protein coupled receptor 4

MacromoleculeName: Leucine-rich repeat-containing G-protein coupled receptor 4
type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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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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: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 771783
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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