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- EMDB-43631: Focused refinement map for mini-Gq protein and an active-state st... -

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Basic information

Entry
Database: EMDB / ID: EMD-43631
TitleFocused refinement map for mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Map dataFocused refinement map for mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Sample
  • Complex: 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq protein and single-chain variable fragment (scFv16)
Keywords5-HT2A receptor / serotonin receptor / G protein / GPCR / Lisuride / cryoEM / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBarros-Alvarez X / Kim K / Panova O / Roth BL / Skiniotis G
Funding support United States, 1 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR001119S0092 United States
CitationJournal: To Be Published
Title: 5-HT2AR bound to Lisuride in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Authors: Barros-Alvarez X / Kim K / Panova O / Roth BL / Skiniotis G
History
DepositionFeb 5, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43631.png

Downloads & links

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Map

FileDownload / File: emd_43631.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement map for mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306.756 Å		0.85 Å/pix.
x 360 pix.
= 306.756 Å		0.85 Å/pix.
x 360 pix.
= 306.756 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.7352694 - 1.3906528
Average (Standard dev.)0.00034383492 (±0.019598098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.756 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map for focused refinement of mini-Gq protein...

Fileemd_43631_half_map_1.map
AnnotationHalf map for focused refinement of mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for focused refinement of mini-Gq protein...

Fileemd_43631_half_map_2.map
AnnotationHalf map for focused refinement of mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq ...

EntireName: 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq protein and single-chain variable fragment (scFv16)
Components
  • Complex: 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq protein and single-chain variable fragment (scFv16)

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Supramolecule #1: 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq ...

SupramoleculeName: 5-HT2AR bound to Lisuride in complex with heterotrimeric mini-Gq protein and single-chain variable fragment (scFv16)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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

Concentration15 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / 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: 67.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 57050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ran

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133216
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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