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- PDB-3c6p: Small molecule agonists and antagonists of F-box protein-substrat... -

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Basic information

Entry
Database: PDB / ID: 3c6p
TitleSmall molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling
Components
  • SKP1-like protein 1A
  • TRANSPORT INHIBITOR RESPONSE 1
KeywordsSIGNALING PROTEIN / auxin / ubiquitin ligase / F-box / small molecule / chemical biology / plant physiology / Auxin signaling pathway / Chromosome partition / Cytoplasm / Cytoskeleton / Developmental protein / Ethylene signaling pathway / Nucleus / Ubl conjugation pathway / Cell cycle / Leucine-rich repeat / Plant defense
Function / homology
Function and homology information


auxin receptor activity / auxin binding / pollen maturation / lateral root formation / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin ...auxin receptor activity / auxin binding / pollen maturation / lateral root formation / stamen development / 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 / cellular response to phosphate starvation / inositol hexakisphosphate binding / SCF ubiquitin ligase complex / chromosome segregation / defense response / microtubule cytoskeleton organization / spindle / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / mitochondrion / nucleus / cytosol
Similarity search - Function
Transport inhibitor response 1 domain / Transport inhibitor response 1 protein domain / COI1, F-box / F-box / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like domain superfamily / SKP1 component, dimerisation ...Transport inhibitor response 1 domain / Transport inhibitor response 1 protein domain / COI1, F-box / F-box / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / Monooxygenase / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Alpha-Beta Horseshoe / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2S)-2-(1H-indol-3-yl)pentanoic acid / INOSITOL HEXAKISPHOSPHATE / SKP1-like protein 1A / Protein TRANSPORT INHIBITOR RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTan, X.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling.
Authors: Hayashi, K. / Tan, X. / Zheng, N. / Hatate, T. / Kimura, Y. / Kepinski, S. / Nozaki, H.
History
DepositionFeb 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id ..._chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 14, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other / Structure summary
Category: cell / diffrn_radiation ...cell / diffrn_radiation / exptl_crystal / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_symm_contact / symmetry
Item: _cell.Z_PDB / _diffrn_radiation.pdbx_diffrn_protocol ..._cell.Z_PDB / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SKP1-like protein 1A
B: TRANSPORT INHIBITOR RESPONSE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6294
Polymers84,7512
Non-polymers8772
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.794, 80.386, 125.206
Angle α, β, γ (deg.)90.00, 104.72, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39255
#2: Protein TRANSPORT INHIBITOR RESPONSE 1 / F-box/LRR-repeat protein 1


Mass: 66875.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIR1, FBL1, WEI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q570C0
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical ChemComp-2S3 / (2S)-2-(1H-indol-3-yl)pentanoic acid


Mass: 217.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 79.16 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6
Details: 12-14% PEG 40,000, 100mM BTP pH6.0, 200mM NaCl, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2007
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 49550 / Num. obs: 24753 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.7 Å / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P1M

1p1m


Resolution: 2.7→49.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.787 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.93 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26075 1324 5.1 %RANDOM
Rwork0.18048 ---
obs0.18454 24753 47.78 %-
all-49550 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.07 Å2
2--2.64 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 52 301 5535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225339
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4791.9927243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15623.559222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.07515941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141539
X-RAY DIFFRACTIONr_chiral_restr0.160.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2810.22977
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.23641
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.23
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9831.53352
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67125313
X-RAY DIFFRACTIONr_scbond_it2.84232251
X-RAY DIFFRACTIONr_scangle_it4.5754.51930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 73 -
Rwork0.241 1295 -
obs--34 %

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