[English] 日本語
Yorodumi
- PDB-2p1n: Mechanism of Auxin Perception by the TIR1 Ubiqutin Ligase -

+
Open data


ID or keywords:

Loading...

-
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 / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / stamen development / ethylene-activated signaling pathway / response to jasmonic acid ...auxin receptor activity / auxin binding / lateral root formation / pollen maturation / phragmoplast / gravitropism / jasmonic acid mediated signaling pathway / stamen development / 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 / 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 / : / 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
(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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Non-polymers , 3 types, 528 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.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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