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- PDB-2e29: Solution structure of the GUCT domain from human ATP-dependent RN... -

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Basic information

Entry
Database: PDB / ID: 2.0E+29
TitleSolution structure of the GUCT domain from human ATP-dependent RNA helicase DDX50, DEAD box protein 50
ComponentsATP-dependent RNA helicase DDX50
KeywordsHYDROLASE / ATP binding / Helicase / Nuclear protein / Nucleotide-binding / RNA-binding / GUCT domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RNA helicase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2280 / GUCT / GUCT (NUC152) domain / : / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...Alpha-Beta Plaits - #2280 / GUCT / GUCT (NUC152) domain / : / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / 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 / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsOhnishi, S. / Paakkonen, K. / Guntert, P. / Sato, M. / Koshiba, S. / Harada, T. / Watanabe, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2008
Title: Solution structure of the GUCT domain from human RNA helicase II/Gubeta reveals the RRM fold, but implausible RNA interactions
Authors: Ohnishi, S. / Paakkonen, K. / Koshiba, S. / Tochio, N. / Sato, M. / Kobayashi, N. / Harada, T. / Watanabe, S. / Muto, Y. / Guntert, P. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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
Revision 1.4May 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 DDX50


Theoretical massNumber of molelcules
Total (without water)10,1491
Polymers10,1491
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 DDX50 / DEAD box protein 50 / Nucleolar protein Gu2 / Gu-beta


Mass: 10149.377 Da / Num. of mol.: 1 / Fragment: GUCT domain, residues 8-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX50 / Plasmid: P060403-01 / Production host: Cell-free protein synthesis
References: UniProt: Q9BQ39, 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
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.9mM protein U-15N,13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 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
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9816Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
OPALpKoradi, R.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
Details: HNN and CACO RDC data, obtained from the Pf1 phage system, were used in the torsion angle dynamics calculation.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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