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- EMDB-62408: Striga MAX2-ASK1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62408
TitleStriga MAX2-ASK1 complex
Map dataLocal Resolution Filtered map of apo-ASK1-MAX2 using Relion LocRes algorithm.
Sample
  • Complex: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24
    • Complex: ASK1
      • Protein or peptide: SKP1-like protein 1A
    • Complex: MAX2
      • Protein or peptide: F-box protein
KeywordsStrigolactone / SCF / Ubiquitination / SIGNALING PROTEIN
Function / homology
Function and homology information


phragmoplast / 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 ...phragmoplast / 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 / mitochondrion / nucleus / cytosol
Similarity search - Function
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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
SKP1-like protein 1A / F-box protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Striga hermonthica (purple witchweed)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsVancea AI / Huntington B / Savva CG / Arold ST
Funding support Saudi Arabia, 1 items
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 AI / Huntington B / Steinchen W / Savva CG / Hameed UFS / Arold ST
History
DepositionNov 14, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62408.png

Downloads & links

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Map

FileDownload / File: emd_62408.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal Resolution Filtered map of apo-ASK1-MAX2 using Relion LocRes algorithm.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00539
Minimum - Maximum-0.02223311 - 0.042970575
Average (Standard dev.)0.0000076105475 (±0.00062770286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62408_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of apo-ASK1-MAX2.

Fileemd_62408_additional_1.map
AnnotationSharpened map of apo-ASK1-MAX2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EMReady postprocessed map from unsharpened reference volume of...

Fileemd_62408_additional_2.map
AnnotationEMReady postprocessed map from unsharpened reference volume of apo-ASK1-MAX2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of apo-ASK1-MAX2.

Fileemd_62408_additional_3.map
AnnotationUnsharpened map of apo-ASK1-MAX2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from Refine3D of apo-ASK1-MAX2

Fileemd_62408_half_map_1.map
AnnotationHalf map 1 from Refine3D of apo-ASK1-MAX2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from Refine3D of apo-ASK1-MAX2

Fileemd_62408_half_map_2.map
AnnotationHalf map 2 from Refine3D of apo-ASK1-MAX2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced b...

EntireName: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24
Components
  • Complex: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24
    • Complex: ASK1
      • Protein or peptide: SKP1-like protein 1A
    • Complex: MAX2
      • Protein or peptide: F-box protein

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Supramolecule #1: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced b...

SupramoleculeName: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: ASK1

SupramoleculeName: ASK1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #3: MAX2

SupramoleculeName: MAX2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Striga hermonthica (purple witchweed)

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Macromolecule #1: SKP1-like protein 1A

MacromoleculeName: SKP1-like protein 1A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.876043 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSAKKIVLKS SDGESFEVEE AVALESQTIA HMVEDDCVDN GVPLPNVTSK ILAKVIEYCK RHVEAAASKA EAVEGAATSD DDLKAWDAD FMKIDQATLF ELILAANYLN IKNLLDLTCQ TVADMIKGKT PEEIRTTFNI KNDFTPEEEE EVRRENQWAF E

UniProtKB: SKP1-like protein 1A

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Macromolecule #2: F-box protein

MacromoleculeName: F-box protein / type: protein_or_peptide / ID: 2 / Details: N-terminal 9xHis and Strep-tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Striga hermonthica (purple witchweed)
Molecular weightTheoretical: 85.626188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH SSGWSHPQFE KGGGSGGGSL EVLFQGPLTP KTNYIPFPSP IHQTPFQTDL APMAAAAAAA TTALNDLPDV ILSNIMAGV SDVRSRNSAS LVCHKWYLLE RATRSALTLR GNIRDLFMLP TCFQSTSHLD LSLISPWGHP LTSAADPDSA L IGHLLRHA ...String:
MHHHHHHHHH SSGWSHPQFE KGGGSGGGSL EVLFQGPLTP KTNYIPFPSP IHQTPFQTDL APMAAAAAAA TTALNDLPDV ILSNIMAGV SDVRSRNSAS LVCHKWYLLE RATRSALTLR GNIRDLFMLP TCFQSTSHLD LSLISPWGHP LTSAADPDSA L IGHLLRHA FPSVTSLAIY ARDPSTIHIV VPQWPDLERL KLVRWHQRPQ TDAAGDELKL LISECGTLKS LDLSSFYCWT DD VPAALGS CPTFAANLKS LNLLNSSFSE GFKSDEIKAI TKACPNLREF RASCMFDPRY IGHAGDEALV SISVNCPKLE ILH LADTNA LSSARSDFDP DEREGLGQEE AKINAATLIE VFSGLPLLEE LALDLCNNVR DSGPALEVLN SKCPKLKSVK LGQF HGISL PVESKLDGIA LCQGLESLSI RNVDDLTDMG LIAIGRGCYR LAKFEVYGCK KITVRGMRTM ASLLRKTLVD VKIAA CKKL GAVQSLKALE PIQDRVERLH IDCDWDCPDE EEPSDYFDSA AEYNECDDEM YSVRKRARYT YDLNSSSSGL DVNVEG YDE DKTWARLRYV SLWIFVGQLL TPLVAAGLND CPELEEISIK VEGDCRVLSR PTVREFGLTT LLNYPKLSRM HLDCGDI NG YAHTAPSGQM DLSLWERFYL IGVGHLGLTE LNYWPPQDRD VNQRSLSLPA AGLLQECNRL RKLFIHGTAH EHFMMFFL R IEGLRDVQLR ADYYPAPEND MSTEMRADSC SRFEVALNRR QISDSSGSSG

UniProtKB: F-box protein

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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

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
0.5 mMC9H15O6PTCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 90.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 20175 / Average exposure time: 3.0 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 524247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: SwissModel, initial_model_type: in silico model

5hzg

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9kll:
Striga MAX2-ASK1 complex

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