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- EMDB-64771: NADH bound purinergic receptor P2Y14 in complex with Gi - recepto... -

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Basic information

Entry
Database: EMDB / ID: EMD-64771
TitleNADH bound purinergic receptor P2Y14 in complex with Gi - receptor focused map
Map data
Sample
  • Complex: P2Y purinoceptor 14
    • Protein or peptide: P2Y purinoceptor 14,Soluble cytochrome b562
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled UDP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / hematopoietic stem cell homeostasis / G alpha (i) signalling events / G protein-coupled receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
P2Y14 purinoceptor / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 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
DepositionMay 23, 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_64771.png

Downloads & links

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Map

FileDownload / File: emd_64771.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-4.5088005 - 9.750679
Average (Standard dev.)-0.0014604834 (±0.051486913)
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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Mask #1

Fileemd_64771_msk_1.map
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Additional map: #1

Fileemd_64771_additional_1.map
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Half map: #1

Fileemd_64771_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_64771_half_map_2.map
Projections & Slices
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Sample components

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Entire : P2Y purinoceptor 14

EntireName: P2Y purinoceptor 14
Components
  • Complex: P2Y purinoceptor 14
    • Protein or peptide: P2Y purinoceptor 14,Soluble cytochrome b562

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Supramolecule #1: P2Y purinoceptor 14

SupramoleculeName: P2Y purinoceptor 14 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: P2Y purinoceptor 14,Soluble cytochrome b562

MacromoleculeName: P2Y purinoceptor 14,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLEFLEVLF QGPAINSTST ...String:
MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLEFLEVLF QGPAINSTST QPPDESCSQN LLITQQIIPV LYCMVFIAGI LLNGVSGWIF FYVPSSKSFI IYLKNIVIAD FVMSLTFPFK ILGDSGLGPW QLNVFVCRVS AVLFYVNMYV SIVFFGLISF DRYYKIVKPL WTSFIQSVSY SKLLSVIVWM LMLLLAVPNI ILTNQSVREV TQIKCIELKS ELGRKWHKAS NYIFVAIFWI VFLLLIVFYT AITKKIFKSH LKSSRNSTSV KKKSSRNIFS IVFVFFVCFV PYHIARIPYT KSQTEAHYSC QSKEILRYMK EFTLLLSAAN VCLDPIIYFF LCQPFREILC KKLHIPLKAQ NDLDISRIKR GNTTLESTDT L

UniProtKB: P2Y purinoceptor 14

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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
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / 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: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 514596
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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