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- EMDB-62415: Rice D3-ASK1 complex in presence of ShHTL7 with GR24 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62415
TitleRice D3-ASK1 complex in presence of ShHTL7 with GR24
Map dataSharpened map of the ASK1-OsD3 complex
Sample
  • Complex: Strigolactone signalling complex of AtASK1-OsD3 in the presence of ShHTL7 and GR24
    • Complex: AtASK1
      • Protein or peptide: A. thaliana ASK1
    • Complex: OsD3
      • Protein or peptide: O. sativa MAX2
KeywordsStrigolactone / SCF / Ubiquitination / SIGNALING 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 / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated 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 / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / auxin polar transport / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to light stimulus / chromosome segregation / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / protein ubiquitination / mitochondrion / nucleus / cytosol
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 / S-phase kinase-associated protein 1-like ...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 / 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/LRR-repeat MAX2 homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Oryza sativa (Asian cultivated rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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_62415.png

Downloads & links

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Map

FileDownload / File: emd_62415.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the ASK1-OsD3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 220 pix.
= 160.38 Å		0.73 Å/pix.
x 220 pix.
= 160.38 Å		0.73 Å/pix.
x 220 pix.
= 160.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0104
Minimum - Maximum-0.03646393 - 0.06282379
Average (Standard dev.)0.0002296473 (±0.0021614733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 160.37999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62415_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of the ASK1-OsD3 complex

Fileemd_62415_additional_1.map
AnnotationUnsharpened map of the ASK1-OsD3 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62415_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62415_half_map_2.map
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 AtASK1-OsD3 in the presence o...

EntireName: Strigolactone signalling complex of AtASK1-OsD3 in the presence of ShHTL7 and GR24
Components
  • Complex: Strigolactone signalling complex of AtASK1-OsD3 in the presence of ShHTL7 and GR24
    • Complex: AtASK1
      • Protein or peptide: A. thaliana ASK1
    • Complex: OsD3
      • Protein or peptide: O. sativa MAX2

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Supramolecule #1: Strigolactone signalling complex of AtASK1-OsD3 in the presence o...

SupramoleculeName: Strigolactone signalling complex of AtASK1-OsD3 in the presence of ShHTL7 and GR24
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: AtASK1

SupramoleculeName: AtASK1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #3: OsD3

SupramoleculeName: OsD3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Oryza sativa (Asian cultivated rice)

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Macromolecule #1: A. thaliana ASK1

MacromoleculeName: A. thaliana ASK1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSAKKIVLKS SDGESFEVEE AVALESQTIA HMVEDDCVDN GVPLPNVTSK ILAKVIEYCK RHVEAAASKA EAVEGAATSD DDLKAWDADF MKIDQATLFE LILAANYLNI KNLLDLTCQT VADMIKGKTP EEIRTTFNIK NDFTPEEEEE VRRENQWAFE

UniProtKB: SKP1-like protein 1A

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Macromolecule #2: O. sativa MAX2

MacromoleculeName: O. sativa MAX2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKS DLEVLFQGPG SMAEEEEVEE GRSSSSAILD LPEPLLLHIL SFLTDVRSRH RAALACGRMR AAERATRSEL SLRGDPRSPG FLFLSHAFRF PALEHLDLSL VSPWGHPLLS SVPPCGGGGG GAPSASSSSG MNVYHPEAIS EQNAFIAARL AGCFPAVTSL ...String:
MWSHPQFEKS DLEVLFQGPG SMAEEEEVEE GRSSSSAILD LPEPLLLHIL SFLTDVRSRH RAALACGRMR AAERATRSEL SLRGDPRSPG FLFLSHAFRF PALEHLDLSL VSPWGHPLLS SVPPCGGGGG GAPSASSSSG MNVYHPEAIS EQNAFIAARL AGCFPAVTSL AVYCRDPTTL ANLTPHWQAS LRRVKLVRWH QRPPTLPDGA DLEPLLETCA ALRELDLSEF YCWTEDVVRA LTTHPSATAA LTHLDLGLAA ATDGFKSSEL GPIAASCPNL RKLVAPCLFN PRFSDCVGDD ALLSLATSCP RLTVLRLSEP FEAAANIQRE EAAITVAGLV AFFAALPALE DFTMDLQHNV LEAAPAMEAL ARRCPRIKFL TLGSFQGLCK ASWLHLDGVA VCGGLESLYM KNCQDLTDAS LAAIGRGCRR LAKFGIHGCD LVTSAGIRRL AFTLRPTLKE VTVLHCRLLH TAECLTALSP IRDRIESLEI NCVWNTTEQP CSVANGTTTE CDPEDDELGE VYESAAKKCR YMEFDDLGSW EMLRSLSLWF SAGQLLSPLI SAGLDSCPVL EEISIKVEGD CRTCPRPAPR TIFGLSDLAG FPVLAKMKLD LSEAVGYALT APTGQMDLSL WERFYLHGIE SLQTLYELDY WPPQDKDVHH RSLTLPAVGL IQRCVGLRKL FIHGTTHEHF MTFFLSIPNL RDMQLREDYY PAPENDLMFT EMRAESWLRF EVQLNSRQID DHHHHHH

UniProtKB: F-box/LRR-repeat MAX2 homolog

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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

Concentration0.50 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
1.0 mMC9H15O6PTCEP
5.0 mMC6H5O7-3Citrate
0.005 %C58H114O26Tween-20
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 35 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: 2 / Number real images: 14113 / Average exposure time: 4.5 sec. / Average electron dose: 40.0 e/Å2
Details: 6,741 movies collected at 0 degree tilt from one grid. 7,372 movies collected at 30 degree tilt from another grid.
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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 227282
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5hzg


Chain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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