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- EMDB-54527: Structure of LGR4 with NB21 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54527
TitleStructure of LGR4 with NB21
Map data
Sample
  • Complex: The structure of LGR4 with NB21
    • Protein or peptide: NB21
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: NB52
KeywordsLGR4 / nanobody / MEMBRANE PROTEIN
Function / homology
Function and homology information


metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling / digestive tract development ...metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling / digestive tract development / negative regulation of cold-induced thermogenesis / negative regulation of cytokine production / bone mineralization / hair follicle development / Regulation of FZD by ubiquitination / 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 / spermatogenesis / innate immune response / plasma membrane
Similarity search - Function
Glycoprotein hormone receptor family / 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 / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Glycoprotein hormone receptor family / 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 / 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
Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Camelus bactrianus (Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsWang L / Geng Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of LGR4 with NB21
Authors: Wang L / Geng Y
History
DepositionJul 23, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54527.png

Downloads & links

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Map

FileDownload / File: emd_54527.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.)
1.11 Å/pix.
x 300 pix.
= 331.5 Å		1.11 Å/pix.
x 300 pix.
= 331.5 Å		1.11 Å/pix.
x 300 pix.
= 331.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21928321 - 0.5087264
Average (Standard dev.)0.00017681129 (±0.011139878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 331.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54527_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_54527_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 : The structure of LGR4 with NB21

EntireName: The structure of LGR4 with NB21
Components
  • Complex: The structure of LGR4 with NB21
    • Protein or peptide: NB21
    • Protein or peptide: Leucine-rich repeat-containing G-protein coupled receptor 4
    • Protein or peptide: NB52

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Supramolecule #1: The structure of LGR4 with NB21

SupramoleculeName: The structure of LGR4 with NB21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NB21

MacromoleculeName: NB21 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 13.099553 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VALAESGGGS VAAGGAIRLS CTASGYTYSK YCMGWFRQAP GAERAGVSGI TTGGLSPYYA DSVAGRFTIS RDNIANTLYL QMNSLAPAD TAMYYCAASR LSCSAADFKD FRNFVYWGQG TQVTSA

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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: 87.469375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PCSCDGDRRV DCSGKGLTAV PEGLSAFTQA LDISMNNITQ LPEDAFANFP FLEELQLAGN DLSFIHPKAL SGLKELKVLT LQNNQLKTV PSEAIRGLSA LQSLRLDANH ITSVPEDSFE GLVQLRHLWL DDNSLTEVPV HPLSNLPTLQ ALTLALNKIS S IPDFAFTN ...String:
PCSCDGDRRV DCSGKGLTAV PEGLSAFTQA LDISMNNITQ LPEDAFANFP FLEELQLAGN DLSFIHPKAL SGLKELKVLT LQNNQLKTV PSEAIRGLSA LQSLRLDANH ITSVPEDSFE GLVQLRHLWL DDNSLTEVPV HPLSNLPTLQ ALTLALNKIS S IPDFAFTN LSSLVVLHLH NNKIRSLSQH CFDGLDNLET LDLNYNNLGE FPQAIKALPS LKELGFHSNS ISVIPDGAFD GN PLLRTIH LYDNPLSFVG NSAFHNLSDL HSLVIRGASM VQQFPNLTGT VHLESLTLTG TKISSIPNNL CQEQKMLRTL DLS YNNIRD LPSFNGCHAL EEISLQRNQI YQIKEGTFQG LISLRILDLS RNLIHEIHSR AFATLGPITN LDVSFNELTS FPTE GLNGL NQLKLVGNFK LKEALAAKDF VNLRSLSVPY AYQCCAFAGC DSYANLNTED NSLQDHSVAQ EKGTADAANV TSTLE NEEH SQIIIHCTPS TGAFKPCEYL LGSWMIRLTV WFIFLVALFF NLLVILTTFA SCTSLPSSKL FIGLISVSNL FMGIYT GIL TFLDAVSWGR FAEFGIWWET GSGCKVAGFL AVFSSESAIF LLMLATVERS LSAKDIMKNG KSNHLKQFRV AALLAFL GA TVAGCFPLFH RGEYSASPLC LPFPGGETPS LGFTVTLVLL NSLAFLLMAV IYTKLYCNLE KEDLSENSQS SMIKHVAW L IFTNCIFFCP VAFFSFAPLI TAISISPEIM KSVTLIFFPL PACLNPVLYV FFNPKFKEDW KLLKRRVTKK S

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

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Macromolecule #3: NB52

MacromoleculeName: NB52 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 10.461716 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
YSPYCMGWFR QAPGKAREGV ATVDLDGSTI YADSVKGRFT ISQDNAKNTL YLQMNSLKPE DTAMYYCASR TRAGVTCGLN WAIFSYWGQ GTQVT

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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 TECNAI 10
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 1.944 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 116975
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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