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- PDB-9w3k: GPR151-Legobody complex -

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Basic information

Entry
Database: PDB / ID: 9w3k
TitleGPR151-Legobody complex
Components
  • Fab-8D3-2-H-His
  • Fab_8D3_L
  • G-protein coupled receptor 151
  • Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
  • NB6
KeywordsMEMBRANE PROTEIN / orphan GPCR / cryo-EM / Legobody
Function / homology
Function and homology information


cholinergic synapse / IgG binding / response to acidic pH / regulation of synaptic vesicle exocytosis / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to ischemia ...cholinergic synapse / IgG binding / response to acidic pH / regulation of synaptic vesicle exocytosis / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to ischemia / G protein-coupled receptor activity / positive regulation of immune response / outer membrane-bounded periplasmic space / synaptic vesicle membrane / presynaptic membrane / G protein-coupled receptor signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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
Immunoglobulin G-binding protein G / Immunoglobulin G-binding protein A / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin G-binding protein A / G-protein coupled receptor 151
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Staphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Streptococcus sp. 'group G' (bacteria)
Homo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 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

Downloads & links

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Assembly

Deposited unit
C: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
H: Fab-8D3-2-H-His
L: Fab_8D3_L
A: G-protein coupled receptor 151
B: NB6


Theoretical massNumber of molelcules
Total (without water)175,0565
Polymers175,0565
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 Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / Staphylococcal protein A / SpA / IgG-binding protein G


Mass: 60575.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His tag-MBP(PrAC-PrAD-PrG)
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria), (gene. exp.) Streptococcus ...Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria), (gene. exp.) Streptococcus sp. 'group G' (bacteria)
Gene: malE, Z5632, ECs5017, spa, spa, SAV0111, spg / Strain: Mu50 / ATCC 700699 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0AEY0, UniProt: P38507, UniProt: P0A015, UniProt: P06654
#2: Antibody Fab-8D3-2-H-His


Mass: 27396.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab_8D3_L


Mass: 26317.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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
#5: 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: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 869552 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039553
ELECTRON MICROSCOPYf_angle_d0.50413005
ELECTRON MICROSCOPYf_dihedral_angle_d3.6141295
ELECTRON MICROSCOPYf_chiral_restr0.0411475
ELECTRON MICROSCOPYf_plane_restr0.0041645

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