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- PDB-2p1q: Mechanism of Auxin Perception by the TIR1 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 2p1q
TitleMechanism of Auxin Perception by the TIR1 ubiquitin ligase
Components
  • Auxin-responsive protein IAA7
  • SKP1-like protein 1A
  • TRANSPORT INHIBITOR RESPONSE 1 protein
KeywordsSIGNALING PROTEIN / F-box / leucine rich repeat
Function / homology
Function and homology information


auxin receptor activity / auxin binding / pollen maturation / lateral root formation / gravitropism / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid ...auxin receptor activity / auxin binding / pollen maturation / lateral root formation / gravitropism / stamen development / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / cellular response to phosphate starvation / inositol hexakisphosphate binding / SCF ubiquitin ligase complex / chromosome segregation / defense response / response to wounding / microtubule cytoskeleton organization / spindle / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / mitochondrion / nucleus / cytosol
Similarity search - Function
AUX/IAA protein / Transport inhibitor response 1 domain / Transport inhibitor response 1 protein domain / AUX/IAA domain / AUX/IAA family / COI1, F-box / F-box / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype ...AUX/IAA protein / Transport inhibitor response 1 domain / Transport inhibitor response 1 protein domain / AUX/IAA domain / AUX/IAA family / 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 / : / PB1 domain profile. / 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
1H-INDOL-3-YLACETIC ACID / INOSITOL HEXAKISPHOSPHATE / Auxin-responsive protein IAA7 / SKP1-like protein 1A / Protein TRANSPORT INHIBITOR RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsTan, X. / Calderon-Villalobos, L.I.A. / Sharon, M. / Robinson, C.V. / Estelle, M. / Zheng, N.
CitationJournal: Nature / Year: 2007
Title: Mechanism of auxin perception by the TIR1 ubiquitin ligase.
Authors: Tan, X. / Calderon-Villalobos, L.I. / Sharon, M. / Zheng, C. / Robinson, C.V. / Estelle, M. / Zheng, N.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 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 protein
C: Auxin-responsive protein IAA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1895
Polymers86,3533
Non-polymers8352
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-34 kcal/mol
Surface area29070 Å2
MethodPISA
2
A: SKP1-like protein 1A
B: TRANSPORT INHIBITOR RESPONSE 1 protein
C: Auxin-responsive protein IAA7
hetero molecules

A: SKP1-like protein 1A
B: TRANSPORT INHIBITOR RESPONSE 1 protein
C: Auxin-responsive protein IAA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,37710
Polymers172,7076
Non-polymers1,6704
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area13330 Å2
ΔGint-83 kcal/mol
Surface area56580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.207, 82.472, 125.053
Angle α, β, γ (deg.)90.00, 104.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1423-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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 protein / 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Auxin-responsive protein IAA7 / Indoleacetic acid-induced protein 7 / Auxin resistant 2


Mass: 1601.872 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IAA7 peptide and indole-3-acetic acid are from commercial sources. It naturally occurs in Arabidopsis thaliana
References: UniProt: Q38825

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Non-polymers , 3 types, 772 molecules

#4: 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
#5: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM BTP, 10% 14% PEG 20,000, 200 mM NaCl, and 5 mM DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 69793 / Num. obs: 69793 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.039 / Net I/σ(I): 33
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 2P1M

2p1m


Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.47 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21333 3733 5.1 %RANDOM
Rwork0.17177 ---
obs0.17386 69793 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20.37 Å2
2--1.12 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 49 770 6401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9887796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.566244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.518151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3291542
X-RAY DIFFRACTIONr_chiral_restr0.1370.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024247
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22787
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23909
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2664
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.53630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25825709
X-RAY DIFFRACTIONr_scbond_it2.37332416
X-RAY DIFFRACTIONr_scangle_it3.6084.52087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 219 -
Rwork0.209 4261 -
obs--78.69 %

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