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- PDB-2p1n: Mechanism of Auxin Perception by the TIR1 Ubiqutin Ligase -

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Basic information

Entry
Database: PDB / ID: 2p1n
TitleMechanism of Auxin Perception by the TIR1 Ubiqutin 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 / lateral root formation / pollen maturation / stamen development / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid ...auxin receptor activity / auxin binding / lateral root formation / pollen maturation / stamen development / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / inositol hexakisphosphate binding / negative regulation of DNA recombination / cellular response to phosphate starvation / SCF ubiquitin ligase complex / chromosome segregation / defense response / spindle / microtubule cytoskeleton organization / response to wounding / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / transcription cis-regulatory region binding / cell cycle / DNA-binding transcription factor activity / mitochondrion / nucleus / cytosol
Similarity search - Function
AUX/IAA protein / Transport inhibitor response 1 domain / COI1, F-box / F-box / Transport inhibitor response 1 protein domain / AUX/IAA domain / AUX/IAA family / Monooxygenase - #50 / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily ...AUX/IAA protein / Transport inhibitor response 1 domain / COI1, F-box / F-box / Transport inhibitor response 1 protein domain / AUX/IAA domain / AUX/IAA family / 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 / PB1 domain profile. / PB1 domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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
(2,4-DICHLOROPHENOXY)ACETIC 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: 2.5 Å
AuthorsTan, X. / Calderon-Villalobos, L.I.A. / Sharon, M. / Robinson, C.V. / Estelle, M. / Zheng, C. / Zheng, N.
CitationJournal: Nature / Year: 2007
Title: Mechanism of auxin perception by the TIR1 ubiquitin ligase
Authors: Tan, X. / Calderon-Villalobos, L.I.A. / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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


Theoretical massNumber of molelcules
Total (without water)174,46910
Polymers172,7076
Non-polymers1,7624
Water9,440524
1
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)87,2345
Polymers86,3533
Non-polymers8812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-50 kcal/mol
Surface area29550 Å2
MethodPISA
2
D: SKP1-like protein 1A
E: TRANSPORT INHIBITOR RESPONSE 1 protein
F: Auxin-responsive protein IAA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2345
Polymers86,3533
Non-polymers8812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-52 kcal/mol
Surface area29520 Å2
MethodPISA
3
A: SKP1-like protein 1A
B: TRANSPORT INHIBITOR RESPONSE 1 protein
C: Auxin-responsive protein IAA7
hetero molecules

D: SKP1-like protein 1A
E: TRANSPORT INHIBITOR RESPONSE 1 protein
F: Auxin-responsive protein IAA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,46910
Polymers172,7076
Non-polymers1,7624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area13470 Å2
ΔGint-117 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.665, 82.745, 125.791
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA5 - 1605 - 160
21LYSLYSGLUGLUDD5 - 1605 - 160
12SERSERGLNGLNBB8 - 5788 - 578
22SERSERGLNGLNEE8 - 5788 - 578
13GLNGLNLYSLYSCC1 - 131 - 13
23GLNGLNLYSLYSFF1 - 131 - 13

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 Da / Num. of mol.: 2
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.: 2
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, 2 molecules CF

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


Mass: 1601.872 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: IAA7 peptide is synthesized from commercial source. It naturally occurs in Arabidopsis thaliana
References: UniProt: Q38825

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Non-polymers , 3 types, 528 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID / 2,4-Dichlorophenoxyacetic acid


Mass: 221.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6Cl2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 61845 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.075 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rsym value: 0.405 / % possible all: 98.3

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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: 2.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.042 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27405 3302 5.1 %RANDOM
Rwork0.19458 ---
obs0.19863 61845 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å21.49 Å2
2--1.19 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 98 524 11872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02211603
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7931.98715743
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.24551413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50623.629496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.518152040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8771584
X-RAY DIFFRACTIONr_chiral_restr0.7190.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3090.26066
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3590.27693
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2768
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2131.57337
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.968211523
X-RAY DIFFRACTIONr_scbond_it11.01734918
X-RAY DIFFRACTIONr_scangle_it11.9194.54220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1023medium positional0.540.5
2B4496medium positional0.270.5
3C114medium positional0.40.5
1A1023medium thermal3.522
2B4496medium thermal3.312
3C114medium thermal3.872
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 186 -
Rwork0.236 4049 -
obs--80.07 %

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