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- EMDB-64550: Cryo-EM structure of inactive-DP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64550
TitleCryo-EM structure of inactive-DP1
Map data
Sample
  • Complex: DP1
    • Protein or peptide: Prostaglandin D2 receptor,Soluble cytochrome b562
KeywordsGPCR / DP1 / inactive / MEMBRANE PROTEIN
Function / homology
Function and homology information


prostaglandin J receptor activity / prostaglandin D receptor activity / Prostanoid ligand receptors / adenosine metabolic process / cellular response to prostaglandin D stimulus / male sex determination / sleep / mast cell degranulation / electron transport chain / positive regulation of cytosolic calcium ion concentration ...prostaglandin J receptor activity / prostaglandin D receptor activity / Prostanoid ligand receptors / adenosine metabolic process / cellular response to prostaglandin D stimulus / male sex determination / sleep / mast cell degranulation / electron transport chain / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
Prostaglandin D receptor / Prostanoid receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / Prostaglandin D2 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsXu J / Xu Y / Wu C / Xu HE
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of inactive-DP1
Authors: Xu J / Xu Y / Wu C / Xu HE
History
DepositionMay 12, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64550.png

Downloads & links

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Map

FileDownload / File: emd_64550.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.)
0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.3338797 - 3.112364
Average (Standard dev.)-0.00018588838 (±0.06327901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64550_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64550_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DP1

EntireName: DP1
Components
  • Complex: DP1
    • Protein or peptide: Prostaglandin D2 receptor,Soluble cytochrome b562

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Supramolecule #1: DP1

SupramoleculeName: DP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prostaglandin D2 receptor,Soluble cytochrome b562

MacromoleculeName: Prostaglandin D2 receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.773949 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKSPFYRCQN TTSVEKGNSA VMGGVLFSTG LLGNLLALGL LARSGLGWCS RRPLRPLPSV FYMLVCGLTV TDLLGKCLLS PVVLAAYAQ NRSLRVLAPA LDNSLCQAFA FFMSFFGLSS TLQLLAMALE CWLSLGHPFF YRRHITLRLG ALVAPVVSAF S LAFCALPF ...String:
MKSPFYRCQN TTSVEKGNSA VMGGVLFSTG LLGNLLALGL LARSGLGWCS RRPLRPLPSV FYMLVCGLTV TDLLGKCLLS PVVLAAYAQ NRSLRVLAPA LDNSLCQAFA FFMSFFGLSS TLQLLAMALE CWLSLGHPFF YRRHITLRLG ALVAPVVSAF S LAFCALPF MGFGKFVQYC PGTWCFIQMV HEEGSLSVLG YSVLYSSLMA LLVLATVLCN LGAMRNLYAA RRQLADLEDN WE TLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQ AAAEQL KTTRNAYIQK YLERARSTLL EELDHLLLLA LMTVLFTMCS LPVIYRAYYG AFKDVKEKNR TSEEAEDLRA LRFL SVISI VDPWIFIIFR SPVFRIFFHK IFI

UniProtKB: Prostaglandin D2 receptor, Soluble cytochrome b562, Prostaglandin D2 receptor

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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: 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: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8zvz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41270
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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