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- PDB-2khx: Drosha double-stranded RNA binding motif -

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Basic information

Entry
Database: PDB / ID: 2khx
TitleDrosha double-stranded RNA binding motif
ComponentsRibonuclease 3
KeywordsGENE REGULATION / NUCLEAR PROTEIN / DROSHA / RNA BINDING DOMAIN / Hydrolase
Function / homology
Function and homology information


regulation of miRNA metabolic process / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / ribonuclease III / miRNA metabolic process / primary miRNA processing / ribonuclease III activity / microprocessor complex ...regulation of miRNA metabolic process / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / ribonuclease III / miRNA metabolic process / primary miRNA processing / ribonuclease III activity / microprocessor complex / pre-miRNA processing / MicroRNA (miRNA) biogenesis / termination of RNA polymerase II transcription / SMAD binding / R-SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / regulation of inflammatory response / defense response to Gram-negative bacterium / postsynaptic density / defense response to Gram-positive bacterium / glutamatergic synapse / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
RNase III, double-stranded RNA binding domain, animal / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...RNase III, double-stranded RNA binding domain, animal / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMueller, G.A. / Miller, M. / Ghosh, M. / DeRose, E.F. / London, R.E. / Hall, T.
CitationJournal: Silence / Year: 2010
Title: Solution structure of the Drosha double-stranded RNA-binding domain.
Authors: Mueller, G.A. / Miller, M.T. / Derose, E.F. / Ghosh, M. / London, R.E. / Hall, T.M.
History
DepositionApr 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease 3


Theoretical massNumber of molelcules
Total (without water)9,5901
Polymers9,5901
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease 3 / Ribonuclease III / RNase III / Drosha / p241


Mass: 9589.887 Da / Num. of mol.: 1 / Fragment: Residues 1259-1337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEN, RN3, RNASE3L / Plasmid: pet21c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRR4, ribonuclease III

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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
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D H(CCO)NH
1713D C(CO)NH
181CN-4D simultaneous NOESY
191HB-HE/HD-aromatic

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Sample preparation

DetailsContents: 1-2 mM [U-99% 13C; U-99% 15N] protein, 25 mM [U-2H] TRIS, 100 mM potassium chloride, 1 mM [U-2H] DTT, 1 mM EDTA, 10 uM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-99% 13C; U-99% 15N]1-21
25 mMTRIS-2[U-2H]1
100 mMpotassium chloride-31
1 mMDTT-4[U-2H]1
1 mMEDTA-51
10 uMDSS-61
Sample conditionsIonic strength: 0.125 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: XPLOR-NIH, refine.py Loosened restraints after CYANA calculations
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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