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- EMDB-61673: A3R-Gi complex bound to m6a (receptor focused) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61673
TitleA3R-Gi complex bound to m6a (receptor focused)
Map data
Sample
  • Complex: A3R-Gi complex bound to NECA
KeywordsGPCR / complex / adenosine receptor / adenosine / g protein / SIGNALING PROTEIN
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsOshima HS / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: To Be Published
Title: Structural insight into the agonist selectivity and structure-based engineering of the adenosine A3 receptor
Authors: Oshima HS / Ogawa A / Sano FK / Akasaka H / Kawakami H / Okamoto HH / Iwama A / Nagiri C / Wei F-Y / Shihoya W / Nureki O
History
DepositionSep 24, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61673.png

Downloads & links

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Map

FileDownload / File: emd_61673.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 210 pix.
= 233.1 Å		1.11 Å/pix.
x 210 pix.
= 233.1 Å		1.11 Å/pix.
x 210 pix.
= 233.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0591
Minimum - Maximum-0.16642983 - 0.22212233
Average (Standard dev.)-0.0002689676 (±0.0058792266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 233.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61673_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_61673_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 : A3R-Gi complex bound to NECA

EntireName: A3R-Gi complex bound to NECA
Components
  • Complex: A3R-Gi complex bound to NECA

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Supramolecule #1: A3R-Gi complex bound to NECA

SupramoleculeName: A3R-Gi complex bound to NECA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Ovis aries (sheep)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156891
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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