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- EMDB-43735: Structure of a LGR dimer from Caenorhabditis elegans in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-43735
TitleStructure of a LGR dimer from Caenorhabditis elegans in apo state
Map data
Sample
  • Organelle or cellular component: CeLGR
    • Protein or peptide: G-protein coupled receptors family 1 profile domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
Keywordsglycoprotein hormones / glycoprotein hormone receptors / leucine-rich-repeat-containing GPCRs (LGRs) / Caenorhabditis elegans / dimer / cryo-EM. / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein-hormone receptor activity / G protein-coupled receptor activity / plasma membrane
Similarity search - Function
Glycoprotein hormone receptor family / Leucine rich repeat / 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
G-protein coupled receptors family 1 profile domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsGong Z / Hendrickson WA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH P41 GM116799 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure of an LGR dimer, an evolutionary predecessor of glycoprotein hormone receptors.
Authors: Zhen Gong / Shuobing Chen / Ziao Fu / Brian Kloss / Chi Wang / Jonathan Kim / Oliver B Clarke / Qing R Fan / Wayne A Hendrickson /
Abstract: Glycoprotein hormones (GpHs) produced in the human pituitary act through receptors (GpHRs) in the gonads to support reproduction and in the thyroid for metabolism. GpHs are heterodimeric cystine-knot ...Glycoprotein hormones (GpHs) produced in the human pituitary act through receptors (GpHRs) in the gonads to support reproduction and in the thyroid for metabolism. GpHs are heterodimeric cystine-knot proteins; their receptors bind cognate hormones at an extracellular domain and signal through a transmembrane domain to heterotrimeric G proteins. GpHs and GpHRs have co-evolved from invertebrate counterparts. Structures of the human receptors as isolated for cryogenic electron microscopy (cryo-EM) are all monomeric despite compelling evidence for their functioning as dimers. Here we characterize the homologous receptor from Caenorhabditis elegans. Its biochemical properties are notably similar to those of the thyroid stimulating hormone receptor (TSHR) of humans. Structurally, it is an asymmetric dimer (protomers screw-transformed by 142°/4.1 Å), composed such that only one hormone could bind. This is compatible with the 1:2 asymmetry of negatively cooperative TSH:TSHR complexes and for the transactivation evident from functional complementation of binding-deficient and signaling-deficient GpHRs. By modeling, a symmetrized dimer can bind two hormones as in the 2:2 complexes that support TSHR switches in G-protein usage.
History
DepositionFeb 19, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43735.png

Downloads & links

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Map

FileDownload / File: emd_43735.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018056176 - 2.2186606
Average (Standard dev.)0.00092338765 (±0.022028051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43735_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43735_half_map_2.map
Projections & Slices
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Sample components

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Entire : CeLGR

EntireName: CeLGR
Components
  • Organelle or cellular component: CeLGR
    • Protein or peptide: G-protein coupled receptors family 1 profile domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL

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Supramolecule #1: CeLGR

SupramoleculeName: CeLGR / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 79.3 kDa/nm

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Macromolecule #1: G-protein coupled receptors family 1 profile domain-containing protein

MacromoleculeName: G-protein coupled receptors family 1 profile domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 79.362734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKQN ALSLAQTKHS CMALKAEDGE GCTCKQTKRY GQPECCCMGL IVSQLPTNLT ADVGYLYLHN TSISVITPNF FDKFPSIRE LEIDNSAHLE HIDGSSLSVL SKLRKLSVVK CPNLREISGK LLVNNTRIQN VILKNNGLAT MPSLRMTDAH H VLLDRIDL ...String:
DYKDDDDKQN ALSLAQTKHS CMALKAEDGE GCTCKQTKRY GQPECCCMGL IVSQLPTNLT ADVGYLYLHN TSISVITPNF FDKFPSIRE LEIDNSAHLE HIDGSSLSVL SKLRKLSVVK CPNLREISGK LLVNNTRIQN VILKNNGLAT MPSLRMTDAH H VLLDRIDL SGNKIKFISD SKVRNVKART VVLSENKLIE ISGYAFTESQ FLKLKLNNNP DLRSLSVDAF KNMAGLQTLD LS HTSIDTL PINGLKKLKT LILNDVPTLK SLPSVLSFTD LETAHFTYPH HCCLFKYVDD VTMNDNGKYQ RNAKEIHKRI CDK REQQKV ARRRKRETSG IDFLDMLLKE WTDNSTYTGP DDADDDELPP FVEIGAEPCQ SIGEEVQKYY SNITCYPQPD ALNP CENIV GYPFLRIAVW VVCLAAIVGN IIVWALLGIV YEKRMRMHYL YMINMSVADM VTGIYLAVLA IADAKMSDEY YRHAV WWQT GWGCRAAGFL AVFASELGII SMFLIAFEMS YNTRQSFRGR RLSPKVGVLL MIGGWLFAII MAILPWFDVS SYSESS VCL PLRAATIFDK SYLIFGLSFN FLAFAAMALS YGFIVKMLKE NETREEDRAL ITKMTVLVVT DLICWFPTLF FGFTATI GF PLLSLSSAKF VLVFFFPINA FANPFLYVFF TEVIQHRVRS KTLPVIRRAA ADYKDDDDK

UniProtKB: G-protein coupled receptors family 1 profile domain-containing protein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.01 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72220
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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