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- PDB-8if6: Conformational Dynamics of the D53-D3-D14 Complex in Strigolacton... -

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Basic information

Entry
Database: PDB / ID: 8if6
TitleConformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 20
  • Strigolactone esterase D14
KeywordsPLANT PROTEIN / D14 D3 D53 SL
Function / homology
Function and homology information


bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / strigolactone biosynthetic process / secondary shoot formation / jasmonic acid mediated signaling pathway / auxin polar transport ...bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / strigolactone biosynthetic process / secondary shoot formation / jasmonic acid mediated signaling pathway / auxin polar transport / response to water deprivation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to light stimulus / cullin family protein binding / Hydrolases; Acting on ester bonds / hydrolase activity / protein ubiquitination / nucleus / cytoplasm
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / 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 / Alpha/beta hydrolase family ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / 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 / Alpha/beta hydrolase family / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Alpha/beta hydrolase fold-1 / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Strigolactone esterase D14 / F-box/LRR-repeat MAX2 homolog / SKP1-like protein 20
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.09 Å
AuthorsLiu, S.M. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Cell Physiol / Year: 2023
Title: Conformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling.
Authors: Simiao Liu / Jia Wang / Bin Song / Xinqi Gong / Huihui Liu / Qingliang Hu / Junhui Zhang / Qianqian Li / Jie Zheng / Hongwei Wang / H Eric Xu / Jiayang Li / Bing Wang /
Abstract: Strigolactones (SLs) play fundamental roles in regulating plant architecture, which is a major factor determining crop yield. The perception and signal transduction of SLs require the formation of a ...Strigolactones (SLs) play fundamental roles in regulating plant architecture, which is a major factor determining crop yield. The perception and signal transduction of SLs require the formation of a complex containing the receptor DWARF14 (D14), an F-box protein D3 and a transcriptional regulator D53 in an SL-dependent manner. Structural and biochemical analyses of D14 and its orthologs DAD2 and AtD14, D3 and the complexes of ASK1-D3-AtD14 and D3CTH-D14 have made great contributions to understanding the mechanisms of SL perception. However, structural analyses of D53 and the D53-D3-D14 holo-complex are challenging, and the biochemical mechanism underlying the complex assembly remains poorly understood. Here, we found that apo-D53 was rather flexible and reconstituted the holo-complex containing D53, S-phase kinase-associated protein 1 (SKP1), D3 and D14 with rac-GR24. The cryo-electron microscopy (cryo-EM) structure of SKP1-D3-D14 in the presence of D53 was analyzed and superimposed on the crystal structure of ASK1-D3-AtD14 without D53. No large conformational rearrangement was observed, but a 9Å rotation appeared between D14 and AtD14. Using hydrogen-deuterium exchange monitored by mass spectrometry, we analyzed dynamic motifs of D14, D3 and D53 in the D53-SKP1-D3-D14 complex assembly process and further identified two potential interfaces in D53 that are located in the N and D2 domains, respectively. Together, our results uncovered the dynamic conformational changes and built a model of the holo-complex D53-SKP1-D3-D14, offering valuable information for the biochemical and genetic mechanisms of SL perception and signal transduction.
History
DepositionFeb 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
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Revision 1.1Aug 30, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Sep 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box/LRR-repeat MAX2 homolog
C: Strigolactone esterase D14
B: SKP1-like protein 20


Theoretical massNumber of molelcules
Total (without water)132,0713
Polymers132,0713
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein F-box/LRR-repeat MAX2 homolog / F-box and leucine-rich repeat MAX2 homolog / Protein DWARF 3


Mass: 79308.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5VMP0
#2: Protein Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2


Mass: 33545.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#3: Protein SKP1-like protein 20 / SKP1-like 20


Mass: 19217.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: SKP20, OSK20, Os09g0539500, LOC_Os09g36830, B1274F11.9, OsJ_30167
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q651E8
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Plant protein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 7.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42499 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048877
ELECTRON MICROSCOPYf_angle_d0.67512068
ELECTRON MICROSCOPYf_dihedral_angle_d5.0531222
ELECTRON MICROSCOPYf_chiral_restr0.0431383
ELECTRON MICROSCOPYf_plane_restr0.0071572

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