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- PDB-9w3l: Cryo-EM structure of GPR151-Nb6 complex -

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Basic information

Entry
Database: PDB / ID: 9w3l
TitleCryo-EM structure of GPR151-Nb6 complex
Components
  • G-protein coupled receptor 151
  • NB6
KeywordsMEMBRANE PROTEIN / orphan GPCR / cryo-EM / GPR151
Function / homology
Function and homology information


cholinergic synapse / response to acidic pH / regulation of synaptic vesicle exocytosis / response to ischemia / G protein-coupled receptor activity / positive regulation of immune response / synaptic vesicle membrane / presynaptic membrane / G protein-coupled receptor signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
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
G-protein coupled receptor 151
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSong, Q.Q. / Cong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Decoding the structure of GPR151 via NELiS.
Authors: Yumeng Wang / Luyu Fan / Qianqian Song / Yaning Li / Jiayu Jin / Qiaoyu Zhao / Weijie Gu / Xiangyi Shi / Dianfan Li / Yao Cong / Sheng Wang /
Abstract: Structure determination of orphan G protein-coupled receptors (GPCRs) is hindered by lack of known ligands and their inherent instability during purification. Conventional thermostability screening ...Structure determination of orphan G protein-coupled receptors (GPCRs) is hindered by lack of known ligands and their inherent instability during purification. Conventional thermostability screening requires ligands or purified protein, limiting its utility for orphan GPCRs. Here, we present the Nb6-Enabled Ligand-Free Stabilization Platform (NELiS)-a ligand- and purification-independent method for identifying stabilizing mutations. Applied to GPR151, an orphan GPCR enriched in habenula and implicated in neuropsychiatric disorders, NELiS identified four mutations that significantly improved thermostability and expression, allowing receptor purification. Using the stabilized and purified receptor, we further found a high-affinity, GPR151-specific nanobody that facilitated structural determination. Structural analysis revealed unconventional activation-resistant features across canonical motifs and an autoinhibitory N-terminal region occupying the orthosteric pocket. Functional studies confirmed a unique activation mechanism and the critical role of the N terminus in receptor maturation and trafficking. These results establish NELiS as a generalizable tool for structural and functional investigation of orphan GPCRs.
History
DepositionJul 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein coupled receptor 151
B: NB6


Theoretical massNumber of molelcules
Total (without water)60,7662
Polymers60,7662
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: Protein G-protein coupled receptor 151 / G-protein coupled receptor PGR7 / GPCR-2037 / Galanin receptor 4 / Galanin-receptor-like protein / GalRL


Mass: 46708.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR151, GALR4, GALRL, PGR7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TDV0
#2: Antibody NB6


Mass: 14057.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Production host: Spodoptera frugiperda (fall armyworm)
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

ComponentName: GPR151-Legobody complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Spodoptera frugiperda (fall armyworm)7108
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 47.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2cryoSPARCparticle selection
3PHENIX1.20.1_4487model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 869552 / Symmetry type: POINT
RefinementHighest resolution: 2.76 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033095
ELECTRON MICROSCOPYf_angle_d0.5634225
ELECTRON MICROSCOPYf_dihedral_angle_d3.626427
ELECTRON MICROSCOPYf_chiral_restr0.041500
ELECTRON MICROSCOPYf_plane_restr0.006517

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