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- EMDB-37748: Cryo-EM Structure of human Sphingosine 1-phosphate receptor 3 com... -

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Basic information

Entry
Database: EMDB / ID: EMD-37748
TitleCryo-EM Structure of human Sphingosine 1-phosphate receptor 3 complex from Biortus
Map data
Sample
  • Complex: human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16
KeywordsS1PR3 / GPCR complex / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsCao S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2022
Title: Structural insights into sphingosine-1-phosphate recognition and ligand selectivity of S1PR3-Gi signaling complexes.
Authors: Chang Zhao / Lin Cheng / Wei Wang / Heli Wang / Yongbo Luo / Yuying Feng / Xuehui Wang / Hong Fu / Ye Cai / Shengyong Yang / Ping Fu / Wei Yan / Zhenhua Shao /
History
DepositionOct 11, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37748.png

Downloads & links

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Map

FileDownload / File: emd_37748.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 288 pix.
= 266.4 Å		0.93 Å/pix.
x 288 pix.
= 266.4 Å		0.93 Å/pix.
x 288 pix.
= 266.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.925 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.019257557 - 1.9511126
Average (Standard dev.)0.0010361664 (±0.020283142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37748_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_37748_additional_1.map
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Half map: #1

Fileemd_37748_half_map_1.map
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Half map: #2

Fileemd_37748_half_map_2.map
Projections & Slices
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Sample components

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Entire : human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16

EntireName: human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16
Components
  • Complex: human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16

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Supramolecule #1: human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16

SupramoleculeName: human Sphingosine 1-phosphate receptor 3 complexed with Gi and scfv16
type: complex / ID: 1 / Parent: 0
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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

31345

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 641891
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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