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- PDB-2doa: Solution structure of the helical domain in human Eleven-nineteen... -

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Basic information

Entry
Database: PDB / ID: 2doa
TitleSolution structure of the helical domain in human Eleven-nineteen lysine-rich leukemia protein ELL
ComponentsRNA polymerase II elongation factor ELL
KeywordsTRANSCRIPTION / elongation factor / C19orf17 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


euchromatin => GO:0000791 / histone locus body / negative regulation of phosphatase activity / snRNA transcription by RNA polymerase III / snRNA transcription by RNA polymerase II / positive regulation of DNA-templated transcription, elongation / positive regulation of transcription by RNA polymerase III / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery ...euchromatin => GO:0000791 / histone locus body / negative regulation of phosphatase activity / snRNA transcription by RNA polymerase III / snRNA transcription by RNA polymerase II / positive regulation of DNA-templated transcription, elongation / positive regulation of transcription by RNA polymerase III / 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 / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / phosphatase binding / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Cajal body / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / in utero embryonic development / transcription by RNA polymerase II / nuclear speck / nucleoplasm
Similarity search - Function
RNA polymerase II elongation factor ELL / E3 ubiquitin-protein ligase / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / E3 ubiquitin-protein ligase ELL-like / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...RNA polymerase II elongation factor ELL / E3 ubiquitin-protein ligase / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / E3 ubiquitin-protein ligase ELL-like / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase II elongation factor ELL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the helical domain in human Eleven-nineteen lysine-rich leukemia protein ELL
Authors: Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 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: RNA polymerase II elongation factor ELL


Theoretical massNumber of molelcules
Total (without water)11,4931
Polymers11,4931
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 RNA polymerase II elongation factor ELL / Eleven-nineteen lysine-rich leukemia protein


Mass: 11493.100 Da / Num. of mol.: 1 / Fragment: helical domain, residues 6-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: ELL, C19orf17 / Plasmid: P051025-06 / References: UniProt: P55199

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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: 1mM protein; 20mM d-Tris-HCL(pH 7.0); 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: 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
NMRPipe2002Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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