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- PDB-9kld: Strigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 2) with... -

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Basic information

Entry
Database: PDB / ID: 9kld
TitleStrigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 2) 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 / seed germination / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway ...response to strigolactone / response to karrikin / seedling development / phragmoplast / seed germination / jasmonic acid mediated signaling pathway / 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 / 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: 2.9 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: To Be Published
Title: Mechanism of cooperative strigolactone perception by the MAX2 ubiquitin ligase-receptor-substrate complex
Authors: Vancea, A.I. / Huntington, B. / Steinchen, W. / Savva, C.G. / Hameed, U.F.S. / Arold, S.T.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Sep 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
B: SKP1-like protein 1A
A: Hyposensitive to light 7
C: F-box protein
D: Protein SUPPRESSOR OF MAX2 1
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 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
#2: 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 / Details (production host): Ampicillin / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3PNA2
#3: 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
#4: 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 and C-terminal Strep tag / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SMAX1, At5g57710, MRI1.7 / Plasmid: pQlinkH / Details (production host): Ampicillin / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FHH2
#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, #41RECOMBINANT
3MAX2-HTL7COMPLEX#2-#31RECOMBINANT
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80483 / 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_d0.0039791
ELECTRON MICROSCOPYf_angle_d0.54113263
ELECTRON MICROSCOPYf_dihedral_angle_d5.1591334
ELECTRON MICROSCOPYf_chiral_restr0.0411517
ELECTRON MICROSCOPYf_plane_restr0.0031704

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