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- EMDB-62911: Cryo-EM structure of apo GPR50 with BRIL fusion, anti-BRIL Fab, a... -

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Basic information

Entry
Database: EMDB / ID: EMD-62911
TitleCryo-EM structure of apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
Map data
Sample
  • Complex: apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
    • Complex: anti-Fab Nb
      • Protein or peptide: anti-Fab Nb
    • Complex: anti-BRIL Fab
      • Protein or peptide: anti-BRIL Fab Light Chain
      • Protein or peptide: anti-BRIL Fab Heavy Chain
    • Complex: GPR50
      • Protein or peptide: Melatonin-related receptor,Soluble cytochrome b562
KeywordsG-protein coupled receptor / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


melatonin receptor activity / electron transport chain / G protein-coupled receptor activity / cell-cell signaling / electron transfer activity / periplasmic space / postsynaptic density / iron ion binding / G protein-coupled receptor signaling pathway / heme binding ...melatonin receptor activity / electron transport chain / G protein-coupled receptor activity / cell-cell signaling / electron transfer activity / periplasmic space / postsynaptic density / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / nucleoplasm / plasma membrane
Similarity search - Function
Melatonin-related receptor 1X / Melatonin receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Soluble cytochrome b562 / Melatonin-related receptor
Similarity search - Component
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsShin J / Cho Y
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Mol Cells / Year: 2026
Title: Structure of the melatonin-related orphan receptor, GPR50.
Authors: Jinwoo Shin / Dongyoung Baek / Jihan Kim / Junhyeon Park / Eunyoung Jeong / Yoojoong Kim / Young Jin Kim / Yunje Cho /
Abstract: GPR50 is an orphan GPCR that belongs to the member of melatonin-related receptor family. GPR50 plays roles in various physiological processes, including cancer progression, Notch signaling, and ...GPR50 is an orphan GPCR that belongs to the member of melatonin-related receptor family. GPR50 plays roles in various physiological processes, including cancer progression, Notch signaling, and insulin, leptin, and glucocorticoid signaling. GPR50 forms a complex with melatonin receptor type 1A or 1B, and regulates signaling activity of melatonin receptor type 1A. Although endogenous agonists have not been characterized, GPR50 may have its own signaling activity, which is undefined at present. In this study, in an attempt to characterize the orphan activity of GPR50, we determined the 3.4 Å structure of ligand-free GPR50 using cryo-electron microscopy. We showed that GPR50 exhibits moderate constitutive activity through interaction with Gα. The structure reveals a putative ligand binding pocket and ligand access channels of GPR50 that differ from those of melatonin receptors. Based on the comparison with the AlphaFold3-predicted active state, we propose an activation mechanism of GPR50. Our findings could serve as a platform in identifying the synthetic or endogenous ligands of GPR50, providing insights into the elusive G-protein-dependent signaling of GPR50.
History
DepositionDec 30, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62911.png

Downloads & links

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Map

FileDownload / File: emd_62911.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 340.495 Å		0.85 Å/pix.
x 400 pix.
= 340.495 Å		0.85 Å/pix.
x 400 pix.
= 340.495 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-4.799979 - 6.728179
Average (Standard dev.)-0.0004832831 (±0.06832219)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.4952 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_62911_additional_1.map
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Additional map: #2

Fileemd_62911_additional_2.map
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Additional map: #1

Fileemd_62911_additional_3.map
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Half map: #2

Fileemd_62911_half_map_1.map
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Half map: #1

Fileemd_62911_half_map_2.map
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Sample components

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Entire : apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex

EntireName: apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
Components
  • Complex: apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
    • Complex: anti-Fab Nb
      • Protein or peptide: anti-Fab Nb
    • Complex: anti-BRIL Fab
      • Protein or peptide: anti-BRIL Fab Light Chain
      • Protein or peptide: anti-BRIL Fab Heavy Chain
    • Complex: GPR50
      • Protein or peptide: Melatonin-related receptor,Soluble cytochrome b562

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Supramolecule #1: apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex

SupramoleculeName: apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 127.6 kDa/nm

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Supramolecule #2: anti-Fab Nb

SupramoleculeName: anti-Fab Nb / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: anti-BRIL Fab

SupramoleculeName: anti-BRIL Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: GPR50

SupramoleculeName: GPR50 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: anti-Fab Nb

MacromoleculeName: anti-Fab Nb / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.727252 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MGSQVQLQES GGGLVQPGGS LRLSCAASGR TISRYAMSWF RQAPGKEREF VAVARRSGDG AFYADSVQG RFTVSRDDAK NTVYLQMNSL KPEDTAVYYC AIDSDTFYSG SYDYWGQGTQ VTVSSGGDDD DKSNSWSHPQ F EK

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Macromolecule #2: anti-BRIL Fab Light Chain

MacromoleculeName: anti-BRIL Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.638656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVSAIVLYVL LAAAAHSAFA ADPSDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQYLYYS LVTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC L LNNFYPRE ...String:
MVSAIVLYVL LAAAAHSAFA ADPSDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQYLYYS LVTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRG

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Macromolecule #3: anti-BRIL Fab Heavy Chain

MacromoleculeName: anti-BRIL Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.174799 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVSAIVLYVL LAAAAHSAFA ADPEISEVQL VESGGGLVQP GGSLRLSCAA SGFNVVDFSL HWVRQAPGKG LEWVAYISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWGYWP GEPWWKAFDY WGQGTLVTVS SASTKGPSVF P LAPSSKST ...String:
MVSAIVLYVL LAAAAHSAFA ADPEISEVQL VESGGGLVQP GGSLRLSCAA SGFNVVDFSL HWVRQAPGKG LEWVAYISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWGYWP GEPWWKAFDY WGQGTLVTVS SASTKGPSVF P LAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PS NTKVDKK VEPKSHHHHH HHHLVPRGSE NLYFQSNSPS RLEEELRRRL TE

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Macromolecule #4: Melatonin-related receptor,Soluble cytochrome b562

MacromoleculeName: Melatonin-related receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.741742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLLTALFAY FIVALILAFS VSAKSMGPTL AVPTPYGCIG CKLPQPEYPP ALIIFMFCAM VITIVVDLIG NSMVILAVTK NKKLRNSGN IFVVSLSVAD MLVAIYPYPL MLHAMSIGGW DLSQLQCQMV GFITGLSVVG SIFNIVAIAI NRYCYICHSL Q YERIFSVR ...String:
MRLLTALFAY FIVALILAFS VSAKSMGPTL AVPTPYGCIG CKLPQPEYPP ALIIFMFCAM VITIVVDLIG NSMVILAVTK NKKLRNSGN IFVVSLSVAD MLVAIYPYPL MLHAMSIGGW DLSQLQCQMV GFITGLSVVG SIFNIVAIAI NRYCYICHSL Q YERIFSVR NTCIYLVITW IMTVLAVLPN MYIGTIEYDP RTYTCIFNYL NNPVFTVTIV CIHFVLPLLI VGFCYVRIWT KV LAARRQL ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QID DALKLA NEGKVKEAQA AAEQLKTTRN AYIQKYLERA RSTLDNQLAE VRNFLTMFVI FLLFAVCWCP INVLTVLVAV SPKE MAGKI PNWLYLAAYF IAYFNSCLNA VIYGLLNENF RREYWTIFHA MRHPIIFFSG LISDIREMQE ARTLARARAH ARDQA REQD RAHACRGRGG SLEVLFQGPG SWSHPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Melatonin-related receptor, Soluble cytochrome b562, Melatonin-related receptor

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 608641
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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