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- EMDB-66588: Cryo-EM map of Arabidopsis thaliana SLY1-ASK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-66588
TitleCryo-EM map of Arabidopsis thaliana SLY1-ASK1
Map data
Sample
  • Complex: hetedimer of SLY1-ASK1
  • Other: SLY1
  • Other: ASK1
KeywordsComplex / PLANT PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsWan LH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat Commun / Year: 2026
Title: Structure-guided reprogramming of DELLA turnover for a sustainable Green Revolution in rice.
Authors: Chongyu Xue / Shuang Zhang / Lihao Wan / Zhihui Zhang / Chenchen Zhang / Huangqi Chen / Kai Peng / Yujie Wang / Jie Hu / Xiuhua Gao / Jiamu Du / Xiangdong Fu / Shutong Xu /
Abstract: The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural ...The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural sustainability demands improved nitrogen-use efficiency (NUE). The semi-dwarf Green Revolution varieties (GRVs) characterized by elevated DELLA protein accumulation introduce a fundamental trade-off, increasing lodging resistance and harvest index at the expense of diminished biomass and grain productivity per plant, and require high nitrogen fertilizer inputs to achieve maximum yield potential under high planting density. Here we show that gibberellin (GA)-bound GA-INSENSITIVE DWARF1 (GID1) induces multi-level conformational changes in DELLA protein, affecting its N-terminal DELLA and VHYN/DPT/S and C-terminal VVLV and SAW motifs, thereby facilitating recognition by the SKP1-CULLIN-F-box (SCF) ubiquitin ligase complex and subsequent proteasomal degradation. We also performed structure-guided engineering of the rice SLENDER RICE1 (SLR1)-GID1-GID2 complex and created a series of dwarf alleles exhibiting a continuous spectrum of plant heights in elite cultivars. Notably, the dominant alleles slr1 and slr1 achieved superior yield and enhanced NUE over conventional sd1-containing GRVs. Reprogramming DELLA turnover thus enables to break the long-standing trade-off between high yield and fertilizer dependency, offering a strategy toward a more sustainable and productive Green Revolution.
History
DepositionOct 13, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66588.png

Downloads & links

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Map

FileDownload / File: emd_66588.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.103316136 - 9.913607000000001
Average (Standard dev.)-0.03855431 (±0.20922077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66588_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_66588_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 : hetedimer of SLY1-ASK1

EntireName: hetedimer of SLY1-ASK1
Components
  • Complex: hetedimer of SLY1-ASK1
  • Other: SLY1
  • Other: ASK1

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Supramolecule #1: hetedimer of SLY1-ASK1

SupramoleculeName: hetedimer of SLY1-ASK1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: SLY1

MacromoleculeName: SLY1 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString:
MKRSTTDSDL AGDAHNETNK KMKSTEEEEI GFSNLDENLV YEVLKHVDAK TLAMSSCVSK IWHKTAQDER LWELICTRHW TNIGCGQNQL RSVVLALGGF RRLHSLYLWP LSKPNPRARF GKDELKLTLS LLSIRYYKKM SFTKRPLPES K

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Macromolecule #2: ASK1

MacromoleculeName: ASK1 / type: other / ID: 2 / Classification: other
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString:
MSAKKIVLKS SDGESFEVEE AVALESQTIA HMVEDDCVDN GVPLPNVTSK ILAKVIEYCK RHVEAAASKA EAVEGAATSD DDLKAWDADF MKIDQATLFE LILAANYLNI KNLLDLTCQT VADMIKGKTP EEIRTTFNIK NDFTPEEEEE VRRENQWAFE

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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: METHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 392747
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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