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- EMDB-60991: Cryo-EM structure of GPR158 from Biortus -

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Basic information

Entry
Database: EMDB / ID: EMD-60991
TitleCryo-EM structure of GPR158 from Biortus
Map data
Sample
  • Organelle or cellular component: Metabotropic glycine receptor
Keywordsmembrane protein / cryo-EM / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsShi H / Hu YF / Yang YH / Wang MF / Tian FY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of GPR158 from Biortus
Authors: Shi H / Hu YF
History
DepositionJul 30, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60991.png

Downloads & links

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Map

FileDownload / File: emd_60991.map.gz / Format: CCP4 / Size: 352.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 452 pix.
= 335.836 Å		0.74 Å/pix.
x 452 pix.
= 335.836 Å		0.74 Å/pix.
x 452 pix.
= 335.836 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.64583254 - 1.038723
Average (Standard dev.)-0.00007799355 (±0.01590663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions452452452
Spacing452452452
CellA=B=C: 335.836 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60991_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60991_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_60991_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 : Metabotropic glycine receptor

EntireName: Metabotropic glycine receptor
Components
  • Organelle or cellular component: Metabotropic glycine receptor

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Supramolecule #1: Metabotropic glycine receptor

SupramoleculeName: Metabotropic glycine receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.8 kDa/nm

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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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128493
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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