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- PDB-2lrs: The second dsRBD domain from A. thaliana DICER-LIKE 1 -

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Basic information

Entry
Database: PDB / ID: 2lrs
TitleThe second dsRBD domain from A. thaliana DICER-LIKE 1
ComponentsEndoribonuclease Dicer homolog 1
KeywordsHYDROLASE / miRNA / RNA binding
Function / homology
Function and homology information


ta-siRNA processing / ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / helicase activity / rRNA processing / double-stranded RNA binding / DNA binding / ATP binding / metal ion binding / nucleus
Similarity search - Function
double strand RNA binding domain from DEAD END PROTEIN 1 / Ribonuclease III / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family ...double strand RNA binding domain from DEAD END PROTEIN 1 / Ribonuclease III / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Double Stranded RNA Binding Domain - #20 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease Dicer homolog 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsBurdisso, P. / Suarez, I. / Bersch, B. / Bologna, N. / Palatnik, J. / Boisbouvier, J. / Rasia, R.
CitationJournal: Biochemistry / Year: 2012
Title: Second Double-Stranded RNA Binding Domain of Dicer-like Ribonuclease 1: Structural and Biochemical Characterization.
Authors: Burdisso, P. / Suarez, I.P. / Bologna, N.G. / Palatnik, J.F. / Bersch, B. / Rasia, R.M.
History
DepositionApr 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease Dicer homolog 1


Theoretical massNumber of molelcules
Total (without water)7,9611
Polymers7,9611
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)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Endoribonuclease Dicer homolog 1 / Dicer-like protein 1 / AtDCL1 / Protein ABNORMAL SUSPENSOR 1 / Protein CARPEL FACTORY / Protein ...Dicer-like protein 1 / AtDCL1 / Protein ABNORMAL SUSPENSOR 1 / Protein CARPEL FACTORY / Protein SHORT INTEGUMENTS 1 / Protein SUSPENSOR 1


Mass: 7961.231 Da / Num. of mol.: 1 / Fragment: DRBM 2 domain residues 1837-1907
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DCL1, ASU1, CAF SIN1, SUS1, At1g01040, T25K16.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SP32, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
2343D HNCO
2443D HNCA
2543D HN(CA)CB
2643D HN(CO)CA
2743D HN(COCA)CB
2843D HN(CA)CO
2943D HN(CA)HA
21043D H(CCO)NH
21143D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
21432D 1H-1H NOESY
21532D 1H-1H TOCSY
21622D 15N-IPAP-HSQC
21743D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
1800 mM [U-100% 13C; U-100% 15N] protein, 50 mM HEPES, 0.05 % sodium azide, 1 mM PMSF, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 5 % C12/E5-Hexanol, 10 mM DTT, 1 mM PMSF, 0.05 % sodium azide, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
3800 mM protein, 50 mM sodium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM PMSF, 100% D2O100% D2O
4600 mM [U-100% 13C; U-100% 15N] protein, 100 mM sodium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 1 mM PMSF, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 mMentity-1[U-100% 13C; U-100% 15N]1
50 mMHEPES-21
0.05 %sodium azide-31
1 mMPMSF-41
600 uMentity-5[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate-62
5 %C12/E5-Hexanol-72
10 mMDTT-82
1 mMPMSF-92
0.05 %sodium azide-102
50 mMsodium chloride-112
800 mMentity-123
50 mMsodium phosphate-133
50 mMsodium chloride-143
0.05 %sodium azide-153
1 mMPMSF-163
600 mMentity-17[U-100% 13C; U-100% 15N]4
100 mMsodium phosphate-184
50 mMsodium chloride-194
0.05 %sodium azide-204
1 mMPMSF-214
10 mMDTT-224
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.057ambient 298 K
20.757ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian VXRSVarianVXRS8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges, and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges, and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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