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- EMDB-70512: Cryo-EM Local Refinement Map (GA3-GID1A-RGA) of the Arabidopsis G... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70512
TitleCryo-EM Local Refinement Map (GA3-GID1A-RGA) of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Complex (Alternative Conformation)
Map data
Sample
  • Complex: RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)
KeywordsRGA / GID1A / GA / SLY1 / ASK1 / PLANT PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsDahal P / Sharma K / Borgnia M / Zhou P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural Insights into Proteolysis-Dependent and -Independent Suppression of the Master Regulator DELLA by Gibberellin Receptor
Authors: Dahal P / Wang Y / Hu J / Park J / Forker K / Zhang Z / Sharma K / Borgnia M / Sun TP / Zhou P
History
DepositionMay 6, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70512.png

Downloads & links

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Map

FileDownload / File: emd_70512.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.008 Å		0.85 Å/pix.
x 320 pix.
= 271.008 Å		0.85 Å/pix.
x 320 pix.
= 271.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8469 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.08068355 - 0.1880227
Average (Standard dev.)-0.00019132234 (±0.003661527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70512_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_70512_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70512_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70512_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)

EntireName: RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)
Components
  • Complex: RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)

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Supramolecule #1: RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)

SupramoleculeName: RGA-GID1A-GA3-SLY1-ASK1 Complex (Alternative Conformation)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 556557
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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