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- PDB-2l2m: Solution structure of the second dsRBD of HYL1 -

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Basic information

Entry
Database: PDB / ID: 2l2m
TitleSolution structure of the second dsRBD of HYL1
ComponentsHyponastic leave 1
KeywordsRNA BINDING PROTEIN / PLANT PROTEIN / miRNA / dsRBD
Function / homology
Function and homology information


nuclear dicing body / ta-siRNA processing / leaf proximal/distal pattern formation / response to cytokinin / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / miRNA processing / pre-miRNA processing ...nuclear dicing body / ta-siRNA processing / leaf proximal/distal pattern formation / response to cytokinin / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / miRNA processing / pre-miRNA processing / miRNA binding / double-stranded RNA binding / nuclear speck / identical protein binding / nucleus
Similarity search - Function
AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Double-stranded RNA-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / rosetta full atom relaxation
Model detailsclosest to the average, model 1
AuthorsRasia, R.M. / Mateos, J.L. / Bologna, N.G. / Burdisso, P. / Imbert, L. / Palatnik, J.F. / Boisbouvier, J.
CitationJournal: Biochemistry / Year: 2010
Title: Structure and RNA Interactions of the Plant MicroRNA Processing-Associated Protein HYL1.
Authors: Rasia, R.M. / Mateos, J. / Bologna, N.G. / Burdisso, P. / Imbert, L. / Palatnik, J.F. / Boisbouvier, J.
History
DepositionAug 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyponastic leave 1


Theoretical massNumber of molelcules
Total (without water)8,4751
Polymers8,4751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Hyponastic leave 1


Mass: 8474.767 Da / Num. of mol.: 1 / Fragment: unp residues 97-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g09700, F21M12.9 / Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: O04492

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D HN(COCA)CB
1713D HN(CA)CO
1813D HNCO JCACO
1913D HNCO JNH
11013D HN(CO)CA JCAHA
11123D HNCO JCACO
11223D HNCO JNH
11323D HN(CO)CA JCAHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] hyl1-2, 10 mM DTT, 100 mM sodium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] hyl1-2, 10 mM DTT, 100 mM sodium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 5 % C12E5, 0.2 % Hexanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMhyl1-2-1[U-100% 13C; U-100% 15N]1
10 mMDTT-21
100 mMsodium phosphate-31
50 mMsodium chloride-41
0.05 %sodium azide-51
0.8 mMhyl1-2-6[U-100% 13C; U-100% 15N]2
10 mMDTT-72
100 mMsodium phosphate-82
50 mMsodium chloride-92
0.05 %sodium azide-102
5 %C12E5-112
0.2 %Hexanol-122
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian DirectDrive / Manufacturer: Varian / Model: Direct Drive / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: rosetta full atom relaxation / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 10

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