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- PDB-9l9o: Cryo-EM structure of apo GPR50 with BRIL fusion, anti-BRIL Fab, a... -

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Basic information

Entry
Database: PDB / ID: 9l9o
TitleCryo-EM structure of apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complex
Components
  • Melatonin-related receptor,Soluble cytochrome b562
  • anti-BRIL Fab Heavy Chain
  • anti-BRIL Fab Light Chain
  • anti-Fab Nb
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / G-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)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsShin, J. / Cho, Y.
Funding support Korea, Republic Of, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: anti-Fab Nb
C: anti-BRIL Fab Light Chain
B: anti-BRIL Fab Heavy Chain
A: Melatonin-related receptor,Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)134,2824
Polymers134,2824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody anti-Fab Nb


Mass: 17727.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody anti-BRIL Fab Light Chain


Mass: 25638.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody anti-BRIL Fab Heavy Chain


Mass: 31174.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Protein Melatonin-related receptor,Soluble cytochrome b562 / G protein-coupled receptor 50 / H9 / Cytochrome b-562


Mass: 59741.742 Da / Num. of mol.: 1 / Mutation: M29W,H124I,R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: GPR50, cybC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q13585, UniProt: P0ABE7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1apo GPR50 with BRIL fusion, anti-BRIL Fab, and anti-Fab Nb complexCOMPLEXall0RECOMBINANT
2anti-Fab NbCOMPLEX#11RECOMBINANT
3anti-BRIL FabCOMPLEX#2-#31RECOMBINANT
4GPR50COMPLEX#41RECOMBINANT
Molecular weightValue: 127.6 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Homo sapiens (human)9606
44Homo sapiens (human)9606
54Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Trichoplusia ni (cabbage looper)7111
44Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 608641 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057520
ELECTRON MICROSCOPYf_angle_d0.76510230
ELECTRON MICROSCOPYf_dihedral_angle_d4.431024
ELECTRON MICROSCOPYf_chiral_restr0.0461165
ELECTRON MICROSCOPYf_plane_restr0.0061289

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