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- EMDB-35676: Cryo-EM structure of an orphan GPCR -

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Basic information

Entry
Database: EMDB / ID: EMD-35676
TitleCryo-EM structure of an orphan GPCR
Map data
Sample
  • Complex: Orphan GPCR
    • Protein or peptide: Probable G-protein coupled receptor 179
KeywordsGPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


visual perception / G protein-coupled receptor activity / postsynaptic membrane / dendrite
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
Probable G-protein coupled receptor 179
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsYun Y / Jeong H / Lee HH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structure of human class C orphan GPCR GPR179 involved in visual processing.
Authors: Yaejin Yun / Hyeongseop Jeong / Thibaut Laboute / Kirill A Martemyanov / Hyung Ho Lee /
Abstract: GPR179, an orphan class C GPCR, is expressed at the dendritic tips of ON-bipolar cells in the retina. It plays a pivotal role in the initial synaptic transmission of visual signals from ...GPR179, an orphan class C GPCR, is expressed at the dendritic tips of ON-bipolar cells in the retina. It plays a pivotal role in the initial synaptic transmission of visual signals from photoreceptors, and its deficiency is known to be the cause of complete congenital stationary night blindness. Here, we present the cryo-electron microscopy structure of human GPR179. Notably, the transmembrane domain (TMD) of GPR179 forms a homodimer through the TM1/7 interface with a single inter-protomer disulfide bond, adopting a noncanonical dimerization mode. Furthermore, the TMD dimer exhibits architecture well-suited for the highly curved membrane of the dendritic tip and distinct from the flat membrane arrangement observed in other class C GPCR dimers. Our structure reveals unique structural features of GPR179 TMD, setting it apart from other class C GPCRs. These findings provide a foundation for understanding signal transduction through GPR179 in visual processing and offers insights into the underlying causes of ocular diseases.
History
DepositionMar 17, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35676.png

Downloads & links

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Map

FileDownload / File: emd_35676.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340.495 Å		0.85 Å/pix.
x 400 pix.
= 340.495 Å		0.85 Å/pix.
x 400 pix.
= 340.495 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.19785434 - 1.5985858
Average (Standard dev.)0.004678722 (±0.017601917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.4952 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Orphan GPCR

EntireName: Orphan GPCR
Components
  • Complex: Orphan GPCR
    • Protein or peptide: Probable G-protein coupled receptor 179

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Supramolecule #1: Orphan GPCR

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

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Macromolecule #1: Probable G-protein coupled receptor 179

MacromoleculeName: Probable G-protein coupled receptor 179 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.958773 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGTRGAVMPP PMWGLLGCCF VCAWALGGPR PIRSLPPLSS QVKPGSVPMQ VPLEGAEAAL AYLYSGDAQQ LSQVNCSERY EARGAGAMP GLPPSLQGAA GTLAQAANFL NMLLQANDIR ESSVEEDVEW YQALVRSVAE GDPRVYRALL TFNPPPGASH L QLALQATR ...String:
MGTRGAVMPP PMWGLLGCCF VCAWALGGPR PIRSLPPLSS QVKPGSVPMQ VPLEGAEAAL AYLYSGDAQQ LSQVNCSERY EARGAGAMP GLPPSLQGAA GTLAQAANFL NMLLQANDIR ESSVEEDVEW YQALVRSVAE GDPRVYRALL TFNPPPGASH L QLALQATR TGEETILQDL SGNWVQEENP PGDLDTPALK KRVLTNDLGS LGSPKWPQAD GYVGDTQQVR LSPPFLECQE GR LRPGWLI TLSATFYGLK PDLSPEVRGQ VQMDVDLQSV DINQCASGPG WYSNTHLCDL NSTQCVPLES QGFVLGRYLC RCR PGFYGA SPSGGLEESD FQTTGQFGFP EGRSGRLLQC LPCPEGCTSC MDATPCLVEE AAVLRAAVLA CQACCMLAIF LSML VSYRC RRNKRIWASG VVLLETVLFG FLLLYFPVFI LYFKPSVFRC IALRWVRLLG FAIVYGTIIL KLYRVLQLFL SRTAQ RSAL LSSGRLLRRL GLLLLPVLGF LAVWTVGALE RGIQHAPLVI RGHTPSGRHF YLCHHDRWDY IMVVAELLLL CWGSFL CYA TRAVLSAFHE PRYMGIALHN ELLLSAAFHT ARFVLVPSLH PDWTLLLFFF HTHSTVTTTL ALIFIPKFWK LGAPPRE EM VDEVCEDELD LQHSGSYLGS SIASAWSEHS LDPGDIRDEL KKLYAQLEVH KTKEMAANNP HLPKKRGSSC QGLGRSFM R YLAEFPEALA RQHSFESRAS TVPRARDPPV ATLEVLFQ

UniProtKB: Probable G-protein coupled receptor 179

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.8 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: OTHER / Details: Alphafold model (AF-Q6PRD1-F1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 668157
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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