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- EMDB-63400: Cryo-EM structure of Arabidopsis thaliana RGA in complex with GID... -

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Basic information

Entry
Database: EMDB / ID: EMD-63400
TitleCryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A, SLY1, and ASK2 (focused map)
Map data
Sample
  • Complex: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer
    • Protein or peptide: DELLA protein RGA
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1B
KeywordsGibberellin / DELLA motif / GRAS domain / Plant growth / HORMONE
Function / homology
Function and homology information


regulation of gibberellic acid mediated signaling pathway / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway ...regulation of gibberellic acid mediated signaling pathway / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway / seed germination / regulation of seed germination / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to far red light / response to jasmonic acid / response to auxin / embryo development ending in seed dormancy / auxin-activated signaling pathway / plastid / SCF ubiquitin ligase complex / regulation of protein catabolic process / response to cold / chromosome segregation / promoter-specific chromatin binding / ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus / cytosol
Similarity search - Function
F-box protein SNE / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / F-box domain / F-box-like domain superfamily ...F-box protein SNE / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / F-box domain / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
SKP1-like protein 1B / DELLA protein RGA / F-box protein GID2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsIslam S / Park K / Kwon E / Kim DY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Plant / Year: 2025
Title: Structural insights into gibberellin-mediated DELLA protein degradation.
Authors: Soyaab Islam / Kunwoong Park / Jing Xia / Eunju Kwon / Dong Young Kim /
Abstract: Gibberellin promotes plant growth by downregulating DELLA proteins, which act as growth repressors. In the presence of gibberellin, the gibberellin receptor GID1 binds DELLA proteins, triggering ...Gibberellin promotes plant growth by downregulating DELLA proteins, which act as growth repressors. In the presence of gibberellin, the gibberellin receptor GID1 binds DELLA proteins, triggering their degradation through polyubiquitination by the SCF ubiquitin E3 ligase. Despite extensive studies, the molecular mechanisms by which DELLA proteins assemble with SCF to regulate plant growth remain poorly understood. Here, we present two cryo-electron microscopy structures of the Arabidopsis thaliana DELLA protein RGA in complex with GID1A and GID1A-SLY1-ASK2, respectively. Structural analyses revealed that RGA interacts with GID1A and SLY1 through nonoverlapping binding surfaces, stabilizing the proteins. This suggests that the SCF-RGA-GID1A complex assembles through a stepwise stabilization process induced by gibberellin. Furthermore, structural comparison with GRAS proteins indicates that RGA does not interact with IDD-family transcription factors when bound to SLY1, suggesting that DELLA protein binding to GID1/SLY1 and to transcription factors is mutually exclusive. These findings provide new insights into the gibberellin-mediated regulation of transcription factor activity by DELLA proteins.
History
DepositionFeb 9, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63400.png

Downloads & links

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Map

FileDownload / File: emd_63400.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7451 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0479
Minimum - Maximum-0.2941412 - 0.4551566
Average (Standard dev.)0.0000030554072 (±0.005255293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 298.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63400_msk_1.map
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Half map: #1

Fileemd_63400_half_map_1.map
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Half map: #2

Fileemd_63400_half_map_2.map
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Sample components

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Entire : Partial model of RGA/GID1A/SLY/ASK2 heterotetramer

EntireName: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer
Components
  • Complex: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer
    • Protein or peptide: DELLA protein RGA
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1B

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Supramolecule #1: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer

SupramoleculeName: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: DELLA protein RGA

MacromoleculeName: DELLA protein RGA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 64.100195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKRDHHQFQG RLSNHGTSSS SSSISKDKMM MVKKEEDGGG NMDDELLAVL GYKVRSSEMA EVALKLEQLE TMMSNVQEDG LSHLATDTV HYNPSELYSW LDNMLSELNP PPLPASSNGL DPVLPSPEIC GFPASDYDLK VIPGNAIYQF PAIDSSSSSN N QNKRLKSC ...String:
MKRDHHQFQG RLSNHGTSSS SSSISKDKMM MVKKEEDGGG NMDDELLAVL GYKVRSSEMA EVALKLEQLE TMMSNVQEDG LSHLATDTV HYNPSELYSW LDNMLSELNP PPLPASSNGL DPVLPSPEIC GFPASDYDLK VIPGNAIYQF PAIDSSSSSN N QNKRLKSC SSPDSMVTST STGTQIGGVI GTTVTTTTTT TTAAGESTRS VILVDSQENG VRLVHALMAC AEAIQQNNLT LA EALVKQI GCLAVSQAGA MRKVATYFAE ALARRIYRLS PPQNQIDHCL SDTLQMHFYE TCPYLKFAHF TANQAILEAF EGK KRVHVI DFSMNQGLQW PALMQALALR EGGPPTFRLT GIGPPAPDNS DHLHEVGCKL AQLAEAIHVE FEYRGFVANS LADL DASML ELRPSDTEAV AVNSVFELHK LLGRPGGIEK VLGVVKQIKP VIFTVVEQES NHNGPVFLDR FTESLHYYST LFDSL EGVP NSQDKVMSEV YLGKQICNLV ACEGPDRVER HETLSQWGNR FGSSGLAPAH LGSNAFKQAS MLLSVFNSGQ GYRVEE SNG CLMLGWHTRP LITTSAWKLS TAAY

UniProtKB: DELLA protein RGA

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Macromolecule #2: F-box protein GID2

MacromoleculeName: F-box protein GID2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.628209 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMKRSTTDS DLAGDAHNET NKKMKSTEEE EIGFSNLDEN LVYEVLKHVD AKTLAMSSCV SKIWHKTAQD ERLWELICTR HWTNIGCGQ NQLRSVVLAL GGFRRLHSLY LWPLSKPNPR ARFGKDELKL TLSLLSIRYY EKMSFTKRPL PESK

UniProtKB: F-box protein GID2

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Macromolecule #3: SKP1-like protein 1B

MacromoleculeName: SKP1-like protein 1B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.262406 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMSTVRKIT LKSSDGENFE IDEAVALESQ TIKHMIEDDC TDNGIPLPNV TSKILSKVIE YCKRHVEAAE KSETTADAAA ATTTTTVAS GSSDEDLKTW DSEFIKVDQG TLFDLILAAN YLNIKGLLDL TCQTVADMIK GKTPEEIRKT FNIKNDFTPE E EEEVRREN QWAFE

UniProtKB: SKP1-like protein 1B

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.7 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65737
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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