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- PDB-2bz2: Solution structure of NELF E RRM -

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Basic information

Entry
Database: PDB / ID: 2bz2
TitleSolution structure of NELF E RRM
ComponentsNEGATIVE ELONGATION FACTOR E
KeywordsTRANSCRIPTION REGULATION / NELF E / RNA RECOGNITION MOTIF / ALTERNATIVE SPLICING / NUCLEAR PROTEIN / PHOSPHORYLATION / REPRESSOR / RNA-BINDING / TRANSCRIPTION
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 / XPLOR SIMULATED ANNEALING
AuthorsSchweimer, K. / Rao, J.N. / Neumann, L. / Rosch, P. / Wohrl, B.M.
CitationJournal: Biochem. J. / Year: 2006
Title: Structural studies on the RNA-recognition motif of NELF E, a cellular negative transcription elongation factor involved in the regulation of HIV transcription.
Authors: Rao, J.N. / Neumann, L. / Wenzel, S. / Schweimer, K. / Rosch, P. / Wohrl, B.M.
History
DepositionAug 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / 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_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEGATIVE ELONGATION FACTOR E


Theoretical massNumber of molelcules
Total (without water)13,3841
Polymers13,3841
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 / 80LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein NEGATIVE ELONGATION FACTOR E / NELF E RRM / NELF-E / RD PROTEIN


Mass: 13384.088 Da / Num. of mol.: 1 / Fragment: RNA RECOGNITION MOTIF, RESIDUES 244-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18615

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-EDITED NOESY
12115N- EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL HETERONUCLEAR NMR ON 13C,15N LABELED NELF E RRM

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Sample preparation

DetailsContents: 90% H2O, 10%D2O
Sample conditionsIonic strength: 100 mM / pH: 6.9 / Pressure: 1.0 atm / Temperature: 298.0 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
NameDeveloperClassification
X-PLORBRUNGERrefinement
NMRViewstructure solution
RefinementMethod: XPLOR SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 80 / Conformers submitted total number: 20

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