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- EMDB-65225: Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20 -

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Basic information

Entry
Database: EMDB / ID: EMD-65225
TitleCryo-EM Structure of Human GPR158 Bound to Nanobody Nb20
Map data
Sample
  • Complex: GPR158 complexed with Nb20
    • Complex: GPR158
      • Protein or peptide: Metabotropic glycine receptor
    • Complex: Nanobody
      • Protein or peptide: Nb20
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol
KeywordsGPCR / orphan receptor / nanobody / RGS proteins / signalling receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition ...G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition / transmembrane signaling receptor activity / presynaptic membrane / postsynaptic membrane / G protein-coupled receptor signaling pathway / nucleus / plasma membrane
Similarity search - Function
G-protein coupled receptor 158/179 / : / GPR158/179 extracellular domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsLaboute T / Zucca S / Sial M / Sharma M / Brunori G / Singh S / Singh A / Martemyanov K
Funding support United States, India, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)MH105482 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY034339 United States
Indian Council of Medical ResearchNeuro/2022-NCD-I India
Department of Biotechnology (DBT, India)Neuro/2022-NCD-I India
CitationJournal: To Be Published
Title: Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20
Authors: Laboute T / Zucca S / Sial M / Sharma M / Brunori G / Singh S / Singh A / Martemyanov K
History
DepositionJul 2, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65225.png

Downloads & links

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Map

FileDownload / File: emd_65225.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 340 pix.
= 296.82 Å		0.87 Å/pix.
x 340 pix.
= 296.82 Å		0.87 Å/pix.
x 340 pix.
= 296.82 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0686
Minimum - Maximum-0.38232774 - 0.591497
Average (Standard dev.)0.0008356408 (±0.012778814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 296.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65225_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65225_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPR158 complexed with Nb20

EntireName: GPR158 complexed with Nb20
Components
  • Complex: GPR158 complexed with Nb20
    • Complex: GPR158
      • Protein or peptide: Metabotropic glycine receptor
    • Complex: Nanobody
      • Protein or peptide: Nb20
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol

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Supramolecule #1: GPR158 complexed with Nb20

SupramoleculeName: GPR158 complexed with Nb20 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: GPR158

SupramoleculeName: GPR158 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody

SupramoleculeName: Nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: Metabotropic glycine receptor

MacromoleculeName: Metabotropic glycine receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.251633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE ...String:
MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE PSISRAAITF STDSLSAPAP QVFLQATREE SRILLQDLSS SAPHLANATL ETEWFHGLRR KWRPHLHRRG PN QGPRGLG HSWRRKDGLG GDKSHFKWSP PYLECENGSY KPGWLVTLSS AIYGLQPNLV PEFRGVMKVD INLQKVDIDQ CSS DGWFSG THKCHLNNSE CMPIKGLGFV LGAYECICKA GFYHPGVLPV NNFRRRGPDQ HISGSTKDVS EEAYVCLPCR EGCP FCADD SPCFVQEDKY LRLAIISFQA LCMLLDFVSM LVVYHFRKAK SIRASGLILL ETILFGSLLL YFPVVILYFE PSTFR CILL RWARLLGFAT VYGTVTLKLH RVLKVFLSRT AQRIPYMTGG RVMRMLAVIL LVVFWFLIGW TSSVCQNLEK QISLIG QGK TSDHLIFNMC LIDRWDYMTA VAEFLFLLWG VYLCYAVRTV PSAFHEPRYM AVAVHNELII SAIFHTIRFV LASRLQS DW MLMLYFAHTH LTVTVTIGLL LIPKFSHSSN NPRDDIATEA YEDELDMGRS GSYLNSSINS AWSEHSLDPE DIRDELKK L YAQLEIYKRK KMITNNPHLQ KKRCSKKGLG RSIMRRITEI PETVSRQCSK EDKELEVLFQ

UniProtKB: Metabotropic glycine receptor

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Macromolecule #2: Nb20

MacromoleculeName: Nb20 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 16.722469 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MGSSHHHHHH HHLEVLFQGP AEVQLQESGG GLVQAGGSLR LSCAASGSIG NIYIMGWYRQ TPGPQRELVA TIRTVRWTKY EDYADSVKG RFTISDDDAK NTVYLQMNSL KPEDTAVYYC NYKDYNAPSD GYWGQGTQVT VSSEPKTPKP Q

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 20 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 4 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol / type: ligand / ID: 5 / Number of copies: 1 / Formula: PIE
Molecular weightTheoretical: 836.061 Da
Chemical component information

ChemComp-YBG:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 40 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7she

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121523
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9vor:
Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20

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