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- PDB-7bbb: Solution structure of C-terminal RecA and RRM domains of the DEAD... -

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Basic information

Entry
Database: PDB / ID: 7bbb
TitleSolution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA
ComponentsATP-dependent RNA helicase DbpA
KeywordsRNA BINDING PROTEIN / DEAD box helicase / ribosome biogenesis / RNA
Function / homology
Function and homology information


DNA/RNA helicase activity / 3'-5' RNA helicase activity / ADP binding / ribosome biogenesis / RNA helicase activity / rRNA binding / RNA helicase / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase DbpA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWurm, J.P. / Sprangers, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)616052 Germany
German Research Foundation (DFG)WU 988/1-1 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome.
Authors: Wurm, J.P. / Glowacz, K.A. / Sprangers, R.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DbpA


Theoretical massNumber of molelcules
Total (without water)27,0141
Polymers27,0141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13770 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein ATP-dependent RNA helicase DbpA


Mass: 27014.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Two nonnative glycine residues were introduced at the N-terminus during the cloning procedure
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dbpA, b1343, JW1337 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21693, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic13D HNH NOESY
125isotropic13D HN(CA)CB
135isotropic13D HNCO
145isotropic13D HN(COCA)CB
155isotropic13D HNCA
1115isotropic13D HN(CA)CO
1105isotropic13D H(CCO)NH
195isotropic13D H(CCO)NH
182isotropic13D CCH NOESY
174isotropic13D HCH NOESY
164isotropic13D CNH NOESY
1122isotropic13D HCH NOESY
1131isotropic13D HNH NOESY
1143isotropic12D 1H-13C HSQC
1154isotropic13D CCH NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM U-2H;U-15N;NA-Y;methyl13C1H-ILMVAT DbpA residues 209-457, 20 mM Arginine/Glutamate, 20 mM HEPES, 250 mM NaCl, 1 mM DTT, 95% H2O/5% D2OILMVATY_H2O95% H2O/5% D2O
solution20.8 mM U-2H;U-15N;NA-Y;methyl13C1H-ILMVAT DbpA residues 209-457, 20 mM Arginine/Glutamate, 20 mM HEPES, 250 mM NaCl, 1 mM DTT, 100% D2OILMVATY_D2O100% D2O
solution30.74 mM [U-10% 13C] DbpA residues 209-457, 20 mM Arginine/Glutamate, 20 mM HEPES, 250 mM NaCl, 1 mM DTT, 100% D2O13C_10%100% D2O
solution40.8 mM U-2H;U-15N;methyl13C1H-ILMVA DbpA residues 209-457, 20 mM Arginine/Glutamate, 20 mM HEPES, 250 mM NaCl, 1 mM DTT, 95% H2O/5% D2OILMVA_H2O95% H2O/5% D2O
solution50.74 mM U-13C; U-15N; U-2H;U-13C/U-2H/methyl-1H ILV DbpA residues 209-457, 20 mM Arginine/Glutamate, 20 mM HEPES, 250 mM NaCl, 1 mM DTT, 95% H2O/5% D2O2H13C15N_H2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDbpA residues 209-457U-2H;U-15N;NA-Y;methyl13C1H-ILMVAT1
20 mMArginine/Glutamatenatural abundance1
20 mMHEPESnatural abundance1
250 mMNaClnatural abundance1
1 mMDTTnatural abundance1
0.8 mMDbpA residues 209-457U-2H;U-15N;NA-Y;methyl13C1H-ILMVAT2
20 mMArginine/Glutamatenatural abundance2
20 mMHEPESnatural abundance2
250 mMNaClnatural abundance2
1 mMDTTnatural abundance2
0.74 mMDbpA residues 209-457[U-10% 13C]3
20 mMArginine/Glutamatenatural abundance3
20 mMHEPESnatural abundance3
250 mMNaClnatural abundance3
1 mMDTTnatural abundance3
0.8 mMDbpA residues 209-457U-2H;U-15N;methyl13C1H-ILMVA4
20 mMArginine/Glutamatenatural abundance4
20 mMHEPESnatural abundance4
250 mMNaClnatural abundance4
1 mMDTTnatural abundance4
0.74 mMDbpA residues 209-457U-13C; U-15N; U-2H;U-13C/U-2H/methyl-1H ILV5
20 mMArginine/Glutamatenatural abundance5
20 mMHEPESnatural abundance5
250 mMNaClnatural abundance5
1 mMDTTnatural abundance5
Sample conditionsIonic strength: 290 mM / Label: condition_1 / pH: 7.3 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
NMRFAM-SPARKY1.414W. Leepeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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