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- PDB-1x5p: Solution structure of RRM domain in Parp14 -

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Basic information

Entry
Database: PDB / ID: 1x5p
TitleSolution structure of RRM domain in Parp14
ComponentsNegative elongation factor E
KeywordsRNA BINDING PROTEIN / structure genomics / RRM domain / Parp14 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


NELF complex / positive regulation of protein modification process / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation ...NELF complex / positive regulation of protein modification process / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / localization / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of ERK1 and ERK2 cascade / nuclear body / mRNA binding / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Negative elongation factor E / Negative elongation factor E, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...Negative elongation factor E / Negative elongation factor E, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Negative elongation factor E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RRM domain in Parp14
Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMay 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Negative elongation factor E


Theoretical massNumber of molelcules
Total (without water)10,4081
Polymers10,4081
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 / 100target function, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Negative elongation factor E / NELF-E / RD protein / Parp14


Mass: 10407.619 Da / Num. of mol.: 1 / Fragment: RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: RDBP, NELFE, RD / Plasmid: P041108-01 / References: UniProt: P18615

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.8mM U-15, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / 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
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.925Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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