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- EMDB-47914: Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-47914
TitleHuman P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13 (transmembrane domain)
Map dataHuman P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13 (transmembrane domain)
Sample
  • Complex: GGG bound P2RY8-G13 complex
KeywordsComplex / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBillesboelle CB / Manglik A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13
Authors: LaFlam TN / Billesboelle CB / Matteson T / Wolfreys FD / Lu E / Jinping A / Xu Y / Singhal A / Brandes N / Manglik A / Cyster JG / Ye CJ
History
DepositionNov 14, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47914.png

Downloads & links

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Map

FileDownload / File: emd_47914.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13 (transmembrane domain)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 288 pix.
= 270.72 Å		0.94 Å/pix.
x 288 pix.
= 270.72 Å		0.94 Å/pix.
x 288 pix.
= 270.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.2782764 - 4.7593727
Average (Standard dev.)-0.0003937754 (±0.114434354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 270.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47914_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_47914_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47914_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GGG bound P2RY8-G13 complex

EntireName: GGG bound P2RY8-G13 complex
Components
  • Complex: GGG bound P2RY8-G13 complex

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Supramolecule #1: GGG bound P2RY8-G13 complex

SupramoleculeName: GGG bound P2RY8-G13 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1.4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90243
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 83

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