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- PDB-3c6n: Small molecule agonists and antagonists of F-box protein-substrat... -

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Basic information

Entry
Database: PDB / ID: 3c6n
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 / small molecules / plant physiology / chemical biology / 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 / lateral root formation / pollen maturation / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin ...auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / inositol hexakisphosphate binding / negative regulation of DNA recombination / cellular response to phosphate starvation / 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 / COI1, F-box / F-box / Transport inhibitor response 1 protein domain / Monooxygenase - #50 / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box-like domain superfamily / SKP1 component, dimerisation ...Transport inhibitor response 1 domain / COI1, F-box / F-box / Transport inhibitor response 1 protein domain / Monooxygenase - #50 / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / 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 / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2S8 / 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: 2.6 Å
AuthorsTan, X. / Zheng, N. / Hayashi, K.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)85,7864
Polymers84,7512
Non-polymers1,0352
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.510, 80.661, 125.071
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number5
Space group name H-MC121

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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-2S8 / (2S)-8-[(tert-butoxycarbonyl)amino]-2-(1H-indol-3-yl)octanoic acid


Mass: 374.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 277 K / pH: 6
Details: 12-14% PEG 40,000 1mM BTP pH 6.0, 200mM NaCl, EVAPORATION, temperature 277K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2007
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26541 / % possible obs: 75 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rsym value: 0.0104 / Net I/σ(I): 22.8
Reflection shellHighest resolution: 2.6 Å / % possible all: 75

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Processing

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

1p1m


Resolution: 2.6→49.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.895 / SU B: 22.317 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.484 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1440 5.1 %RANDOM
Rwork0.185 ---
obs0.19 26541 91.8 %-
all-53841 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.01 Å2
2--1.65 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 63 177 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0225100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.4221.9926922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9375622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89823.426216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.05615891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2521539
X-RAY DIFFRACTIONr_chiral_restr0.2330.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023767
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3070.22776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3490.23479
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5061.53206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49525048
X-RAY DIFFRACTIONr_scbond_it4.11532178
X-RAY DIFFRACTIONr_scangle_it6.2144.51874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 52 -
Rwork0.295 1103 -
obs--52.57 %

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