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- PDB-2m3d: NMR structure of the GUCT domain from human DEAD box polypeptide 21 -

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Basic information

Entry
Database: PDB / ID: 2m3d
TitleNMR structure of the GUCT domain from human DEAD box polypeptide 21
ComponentsNucleolar RNA helicase 2
KeywordsHYDROLASE / GUCT domain / RRM fold / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding ...RNA polymerase inhibitor activity / 7SK snRNA binding / R-loop processing / central nervous system projection neuron axonogenesis / positive regulation of myeloid dendritic cell cytokine production / B-WICH complex / miRNA binding / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / snoRNA binding / positive regulation of transcription by RNA polymerase I / response to exogenous dsRNA / Major pathway of rRNA processing in the nucleolus and cytosol / neuron projection maintenance / B-WICH complex positively regulates rRNA expression / microtubule cytoskeleton organization / osteoblast differentiation / rRNA processing / double-stranded RNA binding / chromosome / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / transcription by RNA polymerase II / RNA helicase activity / rRNA binding / RNA helicase / chromatin remodeling / innate immune response / mRNA binding / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #2280 / GUCT / GUCT (NUC152) domain / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Alpha-Beta Plaits - #2280 / GUCT / GUCT (NUC152) domain / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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
Nucleolar RNA helicase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model7
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of the GUCT domain from human DEAD box polypeptide 21 (DDX21)
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionJan 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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: Nucleolar RNA helicase 2


Theoretical massNumber of molelcules
Total (without water)10,6401
Polymers10,6401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Nucleolar RNA helicase 2 / DEAD box protein 21 / Gu-alpha / Nucleolar RNA helicase Gu / Nucleolar RNA helicase II / RH II/Gu


Mass: 10640.144 Da / Num. of mol.: 1 / Fragment: UNP residues 617-710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX21 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q9NR30, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
1514D APSY HACANH
1615D APSY (HA)CA(CO)NH
1715D APSY CBCA(CO)NH

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-99% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM sodium azide, 95 % [U-99% 2H] D2O, 5 % H2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMsodium azide-41
95 %D2O-5[U-99% 2H]1
5 %H2O-61
Sample conditionsIonic strength: 0.798 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert P.structure solution
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
j-UNIOHerrmann, and Wuthrichpeak picking
j-UNIOHerrmann, and Wuthrichchemical shift assignment
j-UNIOHerrmann, and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1566 / NOE intraresidue total count: 441 / NOE long range total count: 458 / NOE medium range total count: 232 / NOE sequential total count: 435
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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