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- PDB-5oun: NMR solution structure of the external DII domain of Rvb2 from Sa... -

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Basic information

Entry
Database: PDB / ID: 5oun
TitleNMR solution structure of the external DII domain of Rvb2 from Saccharomyces cerevisiae
ComponentsRuvB-like protein 2
KeywordsHYDROLASE / ATPase Chaperon Rvb1 Rvb2 RuvBL1 RuvBL2 NMR snoRNP
Function / homology
Function and homology information


R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase ...R2TP complex / Swr1 complex / Ino80 complex / 5'-3' DNA helicase activity / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / rRNA processing / DNA helicase / protein stabilization / chromatin remodeling / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsRouillon, C. / Bragantini, B. / Charpentier, B. / Manival, X. / Quinternet, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0032-02 France
CitationJournal: Biomol NMR Assign / Year: 2018
Title: NMR assignment and solution structure of the external DII domain of the yeast Rvb2 protein.
Authors: Bragantini, B. / Rouillon, C. / Charpentier, B. / Manival, X. / Quinternet, M.
History
DepositionAug 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RuvB-like protein 2


Theoretical massNumber of molelcules
Total (without water)11,8461
Polymers11,8461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 11845.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RVB2, TIH2, TIP49B, YPL235W, P1060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12464, DNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
171isotropic13D HNCO
181isotropic13D HNHA
1111isotropic13D HBHA(CO)NH
1101isotropic13D (H)CCH-TOCSY
191isotropic13D H(CCO)NH
1121isotropic13D C(CO)NH
1131isotropic12D 1H-1H NOESY
1141isotropic13D 1H-13C NOESY
1151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-13C; U-15N] Rvb2DII, 95% H2O/5% D2O / Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: Rvb2DII / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: NaPi 10 mM NaCl 150 mM TCEP 0.5 mM / Ionic strength: 150 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
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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