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- EMDB-41290: Human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 -

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Basic information

Entry
Database: EMDB / ID: EMD-41290
TitleHuman ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Map data
Sample
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Keywordscomplex / GPCR / arrestin / signaling / SIGNALING PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsChen Q / Tesmer JJG
Funding support United States, Denmark, 12 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA254402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161880 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137505 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
Walther Cancer Foundation United States
Robertson Foundation/Cancer Research InstituteIrvington Postdoctoral Fellowship United States
VILLUM FONDEN00025326 Denmark
Ralph W. and Grace M. Showalter Research Trust4480108 United States
CitationJournal: To Be Published
Title: ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding
Authors: Chen Q / Tesmer JJG
History
DepositionJul 19, 2023-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41290.png

Downloads & links

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Map

FileDownload / File: emd_41290.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 379.44 Å		1.05 Å/pix.
x 360 pix.
= 379.44 Å		1.05 Å/pix.
x 360 pix.
= 379.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127
Minimum - Maximum-0.69976556 - 1.0316675
Average (Standard dev.)-0.00004908638 (±0.0121425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 379.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41290_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41290_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 : human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

EntireName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Components
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

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Supramolecule #1: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

SupramoleculeName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)

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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

Concentration0.7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345391
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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