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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: To be published
Title: Cryo-EM structure of an orphan GPCR
Authors: Yun Y / Jeong H / Lee HH
History
DepositionMar 17, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing 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

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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