[English] 日本語
Yorodumi
- PDB-9x5f: Cryo-EM structure of Medicago truncatula GA3-GID1b-DELLA1 ternary... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9x5f
TitleCryo-EM structure of Medicago truncatula GA3-GID1b-DELLA1 ternary complex
Components
  • DELLA protein 1
  • Gibberellin receptor GID1c-like protein
KeywordsPLANT PROTEIN / GA
Function / homology
Function and homology information


response to symbiotic fungus / arbuscular mycorrhizal association / fruit morphogenesis / floral organ morphogenesis / positive regulation of gibberellic acid mediated signaling pathway / regulation of seed dormancy process / negative regulation of seed germination / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway ...response to symbiotic fungus / arbuscular mycorrhizal association / fruit morphogenesis / floral organ morphogenesis / positive regulation of gibberellic acid mediated signaling pathway / regulation of seed dormancy process / negative regulation of seed germination / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway / carboxylesterase activity / response to abscisic acid / cellular response to phosphate starvation / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
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. / : / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. ...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. / : / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
GIBBERELLIN A3 / DELLA protein 1 / Gibberellin receptor GID1c-like protein
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsWan, L.H.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Aug 26, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Gibberellin receptor GID1c-like protein
A: DELLA protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3103
Polymers104,9642
Non-polymers3461
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Gibberellin receptor GID1c-like protein / Putative carboxylesterase


Mass: 39891.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11437344, MTR_7g093950, MtrunA17_Chr7g0259161 / Production host: Escherichia coli (E. coli) / References: UniProt: G7KWD5, carboxylesterase
#2: Protein DELLA protein 1 / MtDELLA1


Mass: 65072.648 Da / Num. of mol.: 1 / Mutation: K175S,R176S,C386S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: DELLA1, MTR_3g065980, MtrunA17_Chr3g0110971 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A396IUP1
#3: Chemical ChemComp-GA3 / GIBBERELLIN A3 / (1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epo xymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid


Mass: 346.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ternary complex of MtG-MtD-GA / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Source (natural)Organism: Medicago truncatula (barrel medic)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: METHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55910 / Symmetry type: POINT
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more