[English] 日本語
Yorodumi
- EMDB-62407: Strigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 4) with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62407
TitleStrigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 4) with covalently bound D-ring
Map dataSharpened map of ASK1-MAX2-HTL7-SMAX1 Class 4
Sample
  • Complex: Strigolactone signalling complex of ASK1-MAX2-HTL-SMAX1 induced by GR24
    • Complex: ASK1
      • Protein or peptide: SKP1-like protein 1A
    • Complex: HTL7-MAX2
      • Protein or peptide: Hyposensitive to light 7
      • Protein or peptide: F-box protein
  • Ligand: (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
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 / metal ion binding / 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 / Alpha/beta hydrolase family / S-phase kinase-associated protein 1-like ...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 / 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
Hyposensitive to light 7 / 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: 2.9 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-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62407.png

Downloads & links

-
Map

FileDownload / File: emd_62407.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ASK1-MAX2-HTL7-SMAX1 Class 4
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: 0.00466
Minimum - Maximum-0.017447632 - 0.034474768
Average (Standard dev.)0.000027106142 (±0.00066084584)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_62407_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: EMReady postprocessed map

Fileemd_62407_additional_1.map
AnnotationEMReady postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map of ASK1-MAX2-HTL7-SMAX1 Class 4

Fileemd_62407_additional_2.map
AnnotationUnsharpened map of ASK1-MAX2-HTL7-SMAX1 Class 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62407_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62407_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: HTL7-MAX2
      • Protein or peptide: Hyposensitive to light 7
      • Protein or peptide: F-box protein
  • Ligand: (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

-
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: #1-#3

-
Supramolecule #2: ASK1

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

-
Supramolecule #3: HTL7-MAX2

SupramoleculeName: HTL7-MAX2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Striga hermonthica (purple witchweed)

-
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

-
Macromolecule #2: Hyposensitive to light 7

MacromoleculeName: Hyposensitive to light 7 / type: protein_or_peptide / ID: 2 / Details: N-terminal 7xHis tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Striga hermonthica (purple witchweed)
Molecular weightTheoretical: 33.472352 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM SSIGLAHNVT ILGSGETTVV LGHGYGTDQS VWKLLVPYLV DDYKVLLYDH MGAGTTNPD YFDFDRYSSL EGYSYDLIAI LEEFQVSKCI YVGHSMSSMA AAVASIFRPD LFHKLVMISP TPRLINTEEY Y GGFEQKVM ...String:
MKHHHHHHHG AAGTSLYKKA GENLYFQGSM SSIGLAHNVT ILGSGETTVV LGHGYGTDQS VWKLLVPYLV DDYKVLLYDH MGAGTTNPD YFDFDRYSSL EGYSYDLIAI LEEFQVSKCI YVGHSMSSMA AAVASIFRPD LFHKLVMISP TPRLINTEEY Y GGFEQKVM DETLRSLDEN FKSLSLGTAP LLLACDLESA AMQEYCRTLF NMRPDIACCI TRMICGLDLR PYLGHVTVPC HI IQSSNDI MVPVAVGEYL RKNLGGPSVV EVMPTEGHLP HLSMPEVTIP VVLRHIRQDI TDH

UniProtKB: Hyposensitive to light 7

-
Macromolecule #3: F-box protein

MacromoleculeName: F-box protein / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: (3E,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}m...

MacromoleculeName: (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
type: ligand / ID: 4 / Number of copies: 1 / Formula: GR2
Molecular weightTheoretical: 298.29 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44453
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
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-9klk:
Strigolactone-induced ASK1-MAX2-HTL7-SMAX1 complex (Class 4) with covalently bound D-ring

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more