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- EMDB-65604: Cryo-EM structure of GPR151-Nb6 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65604
TitleCryo-EM structure of GPR151-Nb6 complex
Map data
Sample
  • Complex: GPR151-Legobody complex
    • Protein or peptide: G-protein coupled receptor 151
    • Protein or peptide: NB6
Keywordsorphan GPCR / cryo-EM / GPR151 / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSong QQ / Cong Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65604.png

Downloads & links

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Map

FileDownload / File: emd_65604.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 400 pix.
= 288. Å		0.72 Å/pix.
x 400 pix.
= 288. Å		0.72 Å/pix.
x 400 pix.
= 288. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.214
Minimum - Maximum-0.0018653461 - 1.9794594
Average (Standard dev.)0.00039454628 (±0.014417546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65604_msk_1.map
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Additional map: #1

Fileemd_65604_additional_1.map
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Half map: #2

Fileemd_65604_half_map_1.map
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Half map: #1

Fileemd_65604_half_map_2.map
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Sample components

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Entire : GPR151-Legobody complex

EntireName: GPR151-Legobody complex
Components
  • Complex: GPR151-Legobody complex
    • Protein or peptide: G-protein coupled receptor 151
    • Protein or peptide: NB6

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Supramolecule #1: GPR151-Legobody complex

SupramoleculeName: GPR151-Legobody complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: G-protein coupled receptor 151

MacromoleculeName: G-protein coupled receptor 151 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.708242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLAAAFADSN SSSMNVSFAH LHFAGGYLPS DSQDWRTIIP ALLVAVCLVG FVGNLCVIGI LLHNAWKGKP SMIHSLILNL SLADLLLLL FSAPIRATAY SKSVWDLGWF VCKSSDWFIH TCMAAKSWTI VVVAKVCFMY ASDPAKQVSI HNYTIWSVLV A IWTVASLL ...String:
MLAAAFADSN SSSMNVSFAH LHFAGGYLPS DSQDWRTIIP ALLVAVCLVG FVGNLCVIGI LLHNAWKGKP SMIHSLILNL SLADLLLLL FSAPIRATAY SKSVWDLGWF VCKSSDWFIH TCMAAKSWTI VVVAKVCFMY ASDPAKQVSI HNYTIWSVLV A IWTVASLL PLPEWFFSTI RHHEGVEMCL VDVPAVAEEF MAMFGKLYPL LAFGLPLFFA SFYYTLMILR LKSVRLLSGS RE KDRNLRR ITRLVLSIAI ISALLWLPEW VAWLWVWHLK AAGPAPPQGF IALSQVLMFS ISAANPLIFL VMSEEFREGL KGV WKWMIT KKPPTVSESQ ETPAGNSEGL PDKVPSPESP ASIPEKEKPS SPSSGKGKTE KAEIPILPDV EQFWHERDTV PSVQ DNDPI PWEHEDQETG EGVK

UniProtKB: G-protein coupled receptor 151, G-protein coupled receptor 151

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Macromolecule #2: NB6

MacromoleculeName: NB6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 14.057646 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MQVQLQESGG GLVQAGESLR LSCAASGTIF RLYDMGWYRR APGKQRELVA SITSGGSTKY GDSVKGRFTI SRDNAKNTVY LQMSSLKPE DTAVYYCNAE YRTGIWEELL DGWGQGTQVT VSSLEHHH

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 869552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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