9X5F | pdb_00009x5f

Cryo-EM structure of Medicago truncatula GA3-GID1b-DELLA1 ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9X5F

This is version 1.1 of the entry. See complete history

Literature

Structure-guided reprogramming of DELLA turnover for a sustainable Green Revolution in rice.

Xue, C.Zhang, S.Wan, L.Zhang, Z.Zhang, C.Chen, H.Peng, K.Wang, Y.Hu, J.Gao, X.Du, J.Fu, X.Xu, S.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-75068-8
  • Primary Citation Related Structures: 
    9X5F, 9X5G, 9X5I

  • PubMed 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 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 Y94A and slr1 Y580A 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.


  • Organizational Affiliation
    • National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 105.31 kDa 
  • Atom Count: 6,121 
  • Modeled Residue Count: 771 
  • Deposited Residue Count: 943 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gibberellin receptor GID1c-like proteinA [auth B]350Medicago truncatulaMutation(s): 0 
Gene Names: 11437344MTR_7g093950MtrunA17_Chr7g0259161
EC: 3.1.1.1
UniProt
Find proteins for G7KWD5 (Medicago truncatula)
Explore G7KWD5 
Go to UniProtKB:  G7KWD5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7KWD5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DELLA protein 1B [auth A]593Medicago truncatulaMutation(s): 3 
Gene Names: DELLA1MTR_3g065980MtrunA17_Chr3g0110971
UniProt
Find proteins for A0A396IUP1 (Medicago truncatula)
Explore A0A396IUP1 
Go to UniProtKB:  A0A396IUP1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A396IUP1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GA3
(Subject of Investigation/LOI)

Query on GA3



Download:Ideal Coordinates CCD File
C [auth B]GIBBERELLIN A3
C19 H22 O6
IXORZMNAPKEEDV-OBDJNFEBSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-07-08 
  • Deposition Author(s): Wan, L.H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000900

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release
  • Version 1.1: 2026-08-19
    Changes: Data collection, Database references