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- EMDB-35402: Conformational Dynamics of the D53-D3-D14 Complex in Strigolacton... -

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Basic information

Entry
Database: EMDB / ID: EMD-35402
TitleConformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling
Map data
Sample
  • Complex: Plant protein complex
    • Protein or peptide: F-box/LRR-repeat MAX2 homolog
    • Protein or peptide: Strigolactone esterase D14
    • Protein or peptide: SKP1-like protein 20
KeywordsD14 D3 D53 SL / PLANT PROTEIN
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 (Asian cultivated rice) / Oryza sativa subsp. japonica (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.09 Å
AuthorsLiu SM / Wang J
Funding support1 items
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, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35402.png

Downloads & links

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Map

FileDownload / File: emd_35402.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 90 pix.
= 196.38 Å		2.18 Å/pix.
x 90 pix.
= 196.38 Å		2.18 Å/pix.
x 90 pix.
= 196.38 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.182 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.8662592 - 1.4293925
Average (Standard dev.)0.008052689 (±0.097452275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 196.37999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35402_half_map_1.map
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Half map: #2

Fileemd_35402_half_map_2.map
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Sample components

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Entire : Plant protein complex

EntireName: Plant protein complex
Components
  • Complex: Plant protein complex
    • Protein or peptide: F-box/LRR-repeat MAX2 homolog
    • Protein or peptide: Strigolactone esterase D14
    • Protein or peptide: SKP1-like protein 20

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Supramolecule #1: Plant protein complex

SupramoleculeName: Plant protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: F-box/LRR-repeat MAX2 homolog

MacromoleculeName: F-box/LRR-repeat MAX2 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 79.308617 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEEEEVEEG RSSSSAILDL PEPLLLHILS FLTDVRSRHR AALACGRMRA AERATRSELS LRGDPRSPGF LFLSHAFRFP ALEHLDLSL VSPWGHPLLS SVPPCGGGGG GAPSASSSSG MNVYHPEAIS EQNAFIAARL AGCFPAVTSL AVYCRDPTTL A NLTPHWQA ...String:
MAEEEEVEEG RSSSSAILDL PEPLLLHILS FLTDVRSRHR AALACGRMRA AERATRSELS LRGDPRSPGF LFLSHAFRFP ALEHLDLSL VSPWGHPLLS SVPPCGGGGG GAPSASSSSG MNVYHPEAIS EQNAFIAARL AGCFPAVTSL AVYCRDPTTL A NLTPHWQA SLRRVKLVRW HQRPPTLPDG ADLEPLLETC AALRELDLSE FYCWTEDVVR ALTTHPSATA ALTHLDLGLA AA TDGFKSS ELGPIAASCP NLRKLVAPCL FNPRFSDCVG DDALLSLATS CPRLTVLRLS EPFEAAANIQ REEAAITVAG LVA FFAALP ALEDFTMDLQ HNVLEAAPAM EALARRCPRI KFLTLGSFQG LCKASWLHLD GVAVCGGLES LYMKNCQDLT DASL AAIGR GCRRLAKFGI HGCDLVTSAG IRRLAFTLRP TLKEVTVLHC RLLHTAECLT ALSPIRDRIE SLEINCVWNT TEQPC SVAN GTTTECDPED DELGEVYESA AKKCRYMEFD DLGSWEMLRS LSLWFSAGQL LSPLISAGLD SCPVLEEISI KVEGDC RTC PRPAPRTIFG LSDLAGFPVL AKMKLDLSEA VGYALTAPTG QMDLSLWERF YLHGIESLQT LYELDYWPPQ DKDVHHR SL TLPAVGLIQR CVGLRKLFIH GTTHEHFMTF FLSIPNLRDM QLREDYYPAP ENDLMFTEMR AESWLRFEVQ LNSRQIDD

UniProtKB: F-box/LRR-repeat MAX2 homolog

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Macromolecule #2: Strigolactone esterase D14

MacromoleculeName: Strigolactone esterase D14 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 33.545023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLRSTHPPPS SPSSSSSGGG GGGGSSASSS SEKTMVGGGG GGGGGSGSAA PSGAKLLQIL NVRVVGSGER VVVLSHGFGT DQSAWSRVL PYLTRDHRVV LYDLVCAGSV NPDHFDFRRY DNLDAYVDDL LAILDALRIP RCAFVGHSVS AMIGILASIR R PDLFAKLV ...String:
MLRSTHPPPS SPSSSSSGGG GGGGSSASSS SEKTMVGGGG GGGGGSGSAA PSGAKLLQIL NVRVVGSGER VVVLSHGFGT DQSAWSRVL PYLTRDHRVV LYDLVCAGSV NPDHFDFRRY DNLDAYVDDL LAILDALRIP RCAFVGHSVS AMIGILASIR R PDLFAKLV LIGASPRFLN DSDYHGGFEL EEIQQVFDAM GANYSAWATG YAPLAVGADV PAAVQEFSRT LFNMRPDISL HV CQTVFKT DLRGVLGMVR APCVVVQTTR DVSVPASVAA YLKAHLGGRT TVEFLQTEGH LPHLSAPSLL AQVLRRALAR Y

UniProtKB: Strigolactone esterase D14

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Macromolecule #3: SKP1-like protein 20

MacromoleculeName: SKP1-like protein 20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 19.217693 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAEAETKAM ITLRSCEGQV FEVAEAVAME SQTIRHMIED KCADTGIPLP NVSAKILSKV IEYCSKHVEA RGGAAAAADG DAPAPAAVE ANKAVEDELK TFDAEFVKVD QSTLFDLILA ANYLNIKGLL DLTCQTVADM IKGKTPEEIR KTFNIKNDFT P EEEEEVRR ENQWAFE

UniProtKB: SKP1-like protein 20

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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: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 0.7000000000000001 µm / Nominal defocus min: 0.5 µm
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: 7.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42499
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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