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- PDB-2kbe: solution structure of amino-terminal domain of Dbp5p -

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Basic information

Entry
Database: PDB / ID: 2kbe
Titlesolution structure of amino-terminal domain of Dbp5p
ComponentsATP-dependent RNA helicase DBP5
KeywordsHYDROLASE / dbp5p / ATP-binding / Cytoplasm / Helicase / Membrane / mRNA transport / Nuclear pore complex / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Translocation / Transport
Function / homology
Function and homology information


cellular bud tip / nuclear pore cytoplasmic filaments / tRNA export from nucleus / ATP-dependent activity, acting on RNA / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / translational termination / cytoplasmic stress granule / protein transport / nuclear membrane ...cellular bud tip / nuclear pore cytoplasmic filaments / tRNA export from nucleus / ATP-dependent activity, acting on RNA / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / translational termination / cytoplasmic stress granule / protein transport / nuclear membrane / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DBP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFan, J.S. / Zhang, J. / Yang, D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides.
Authors: Fan, J.S. / Cheng, Z. / Zhang, J. / Noble, C. / Zhou, Z. / Song, H. / Yang, D.
History
DepositionNov 27, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DBP5


Theoretical massNumber of molelcules
Total (without water)25,2281
Polymers25,2281
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP-dependent RNA helicase DBP5 / DEAD box protein 5 / Helicase CA5/6 / Ribonucleic acid-trafficking protein 8


Mass: 25228.355 Da / Num. of mol.: 1 / Fragment: amino-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DBP5, RAT8, YOR046C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P20449, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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 (H)CCH-TOCSY
1413D HNCA
1514D 15N, 13C-edited NOESY

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Sample preparation

DetailsContents: 20 mM MES, 100 mM potassium acetate, 0.6 mM [U-13C; U-15N] Dbp5p, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES1
100 mMpotassium acetate2
0.6 mMDbp5p[U-13C; U-15N]3
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra, Clorestructure solution
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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