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- PDB-9klv: Strigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 3) with... -

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Basic information

Entry
Database: PDB / ID: 9klv
TitleStrigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 3) with covalently bound D-ring
Components
  • F-box protein
  • Hyposensitive to light 7
  • Protein SUPPRESSOR OF MAX2 1
  • SKP1-like protein 1A
KeywordsSIGNALING PROTEIN / Strigolactone / SCF / Ubiquitination
Function / homology
Function and homology information


response to strigolactone / response to karrikin / seedling development / phragmoplast / jasmonic acid mediated signaling pathway / seed germination / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway ...response to strigolactone / response to karrikin / seedling development / phragmoplast / jasmonic acid mediated signaling pathway / seed germination / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / chromosome segregation / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / hydrolase activity / protein ubiquitination / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
SMAX1 nucleotide binding domain / : / COI1, F-box / F-box / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain ...SMAX1 nucleotide binding domain / : / COI1, F-box / F-box / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Alpha/beta hydrolase family / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / AAA domain (Cdc48 subfamily) / 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 / ATPase, AAA-type, core / Alpha/Beta hydrolase fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-GR2 / Hyposensitive to light 7 / SKP1-like protein 1A / Protein SUPPRESSOR OF MAX2 1 / F-box protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Striga hermonthica (purple witchweed)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVancea, A.I. / Huntington, B. / Savva, C.G. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateURF/1/4039-01-01 & URF/1/4080-01-01 Saudi Arabia
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of cooperative strigolactone perception by the MAX2 ubiquitin ligase-receptor-substrate complex.
Authors: Alexandra I Vancea / Brandon Huntington / Wieland Steinchen / Christos G Savva / Umar F Shahul Hameed / Stefan T Arold /
Abstract: Strigolactones are plant hormones that regulate development and mediate interactions with soil organisms, including the germination of parasitic plants such as Striga hermonthica. Strigolactone ...Strigolactones are plant hormones that regulate development and mediate interactions with soil organisms, including the germination of parasitic plants such as Striga hermonthica. Strigolactone perception by receptors initiates the degradation of transcriptional repressors via E3 ubiquitin ligases, but the mechanistic link between hormone binding and substrate ubiquitination has remained unclear. We determine cryogenic electron microscopy structures of the receptor-ligase-substrate complex, composed of Arabidopsis ASK1 and substrate, and Striga F-box and receptor proteins. Strigolactone hydrolysis by the receptor, which covalently retains the D-ring, is a prerequisite for complex formation. The substrate engages the complex through two domains, forming a dynamic interface that stabilises the receptor-ligase assembly and repositions the ASK1, suggesting a mechanism for efficient ubiquitination. Here, we show how dynamic, multivalent interactions within the receptor-ligase-substrate complex translate hormone perception into targeted protein degradation, providing insight into how plants integrate hormonal signals into developmental decisions.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Protein SUPPRESSOR OF MAX2 1
B: SKP1-like protein 1A
A: Hyposensitive to light 7
C: F-box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,7265
Polymers250,4284
Non-polymers2981
Water00
1


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

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Components

#1: Protein Protein SUPPRESSOR OF MAX2 1 / AtSMXL1


Mass: 113453.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 7xHis tag and C-terminal Strep tag / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SMAX1, At5g57710, MRI1.7 / Plasmid: pQLinkH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FHH2
#2: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17 / Plasmid: pIDS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39255
#3: Protein Hyposensitive to light 7


Mass: 33472.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 7xHis tag / Source: (gene. exp.) Striga hermonthica (purple witchweed) / Plasmid: pQLinkH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3PNA2
#4: Protein F-box protein


Mass: 85626.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 9xHis and Strep tag / Source: (gene. exp.) Striga hermonthica (purple witchweed) / Gene: MAX2 / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: T1RVG4
#5: Chemical ChemComp-GR2 / (3E,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methylidene)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one


Mass: 298.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24COMPLEX#1-#40RECOMBINANT
2ASK1-SMAX1COMPLEX#1-#21RECOMBINANT
3MAX2-HTL7COMPLEX#3-#41RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Striga hermonthica (purple witchweed)68872
32Arabidopsis thaliana (thale cress)3702
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaCl1
30.5 mMTCEPC9H15O6P1
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 165000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingAverage exposure time: 3 sec. / Electron dose: 44 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20175
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17137 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeAccession codeInitial refinement model-ID
11AlphaFoldin silico model
21SwissModelin silico model5HZG2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510938
ELECTRON MICROSCOPYf_angle_d0.6714823
ELECTRON MICROSCOPYf_dihedral_angle_d4.9411490
ELECTRON MICROSCOPYf_chiral_restr0.0441705
ELECTRON MICROSCOPYf_plane_restr0.0051911

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