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- EMDB-63224: UDP-Glucose bound purinergic receptor P2Y14 in complex with Gi - ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-63224
TitleUDP-Glucose bound purinergic receptor P2Y14 in complex with Gi - composite map
Map data
Sample
  • Complex: NADH bound purinergic receptor P2Y14 in complex with heterotrimer Gi - composite map
KeywordsComplex / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsWang TX / Gu QC / Tang WQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural insights into ligand recognition and activation of human purinergic receptor P2Y14.
Authors: Quanchang Gu / Zhenyu Lv / Tianxin Wang / Wenqin Tang / Xuzhen Guo / Xiangling Huang / Fahui Li / Jiangyun Wang /
History
DepositionJan 20, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63224.png

Downloads & links

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Map

FileDownload / File: emd_63224.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.61
Minimum - Maximum-37.292029999999997 - 56.720844
Average (Standard dev.)0.0049369805 (±1.1214639)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NADH bound purinergic receptor P2Y14 in complex with heterotrimer...

EntireName: NADH bound purinergic receptor P2Y14 in complex with heterotrimer Gi - composite map
Components
  • Complex: NADH bound purinergic receptor P2Y14 in complex with heterotrimer Gi - composite map

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Supramolecule #1: NADH bound purinergic receptor P2Y14 in complex with heterotrimer...

SupramoleculeName: NADH bound purinergic receptor P2Y14 in complex with heterotrimer Gi - composite map
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193117
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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