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- PDB-2m1m: Solution structure of the PsIAA4 oligomerization domain reveals i... -

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Basic information

Entry
Database: PDB / ID: 2m1m
TitleSolution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response
ComponentsAuxin-induced protein IAA4
KeywordsTRANSCRIPTION / beta-Grasp (ubiquitin-like)
Function / homology
Function and homology information


auxin-activated signaling pathway / regulation of DNA-templated transcription / nucleus
Similarity search - Function
AUX/IAA protein / AUX/IAA domain / AUX/IAA family / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Auxin-induced protein IAA4
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKovermann, M. / Dinesh, D.C. / Gopalswamy, M. / Abel, S. / Balbach, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response.
Authors: Dinesh, D.C. / Kovermann, M. / Gopalswamy, M. / Hellmuth, A. / Calderon Villalobos, L.I. / Lilie, H. / Balbach, J. / Abel, S.
History
DepositionDec 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin-induced protein IAA4


Theoretical massNumber of molelcules
Total (without water)11,9391
Polymers11,9391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Auxin-induced protein IAA4


Mass: 11938.639 Da / Num. of mol.: 1 / Fragment: UNP residues 86-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Description: The QIAexpressionist (Qiagen) Kit / Gene: IAA4/5 / Plasmid details: pQE expression system / Plasmid: pQE-16 / Production host: Pisum sativum (garden pea) / Strain (production host): M15 / References: UniProt: P49679

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Recominant 6xHis tagged C-terminus of Ps-IAA4 (aa 86-189) protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CA)CB
1613D HN(COCA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11012D 1H-1H NOESY
11113D HNCO
11213D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] PSIAA4, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM magnesium chloride, 1 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPSIAA4-1[U-98% 13C; U-98% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
2 mMmagnesium chloride-41
1 mMDTT-51
Sample conditionsIonic strength: 0.112 / pH: 2.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 84 / Protein psi angle constraints total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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