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- PDB-2bze: NMR Structure of human RTF1 PLUS3 domain. -

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Basic information

Entry
Database: PDB / ID: 2bze
TitleNMR Structure of human RTF1 PLUS3 domain.
ComponentsKIAA0252 PROTEIN
KeywordsTRANSCRIPTION REGULATION / HUMAN RTF1 PLUS3 DOMAIN / TRANSCRIPTION / ELONGATION / PAF1 COMPLEX / HISTONE H3 METHYLATION / H2B UBIQUITINATION / CDC73 / LEO1 / CTR9 / PLUS3 DOMAIN / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


blastocyst growth / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway ...blastocyst growth / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / single-stranded DNA binding / nucleolus / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm
Similarity search - Function
Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA polymerase-associated protein RTF1 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTruffault, V. / Diercks, T. / Ab, E. / De Jong, R.N. / Daniels, M.A. / Kaptein, R. / Folkers, G.E. / Structural Proteomics in Europe (SPINE)
CitationJournal: Structure / Year: 2008
Title: Structure and DNA Binding of the Human Rtf1 Plus3 Domain.
Authors: De Jong, R.N. / Truffault, V. / Diercks, T. / Ab, E. / Daniels, M.A. / Kaptein, R. / Folkers, G.E.
History
DepositionAug 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
Revision 1.4Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 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: KIAA0252 PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,5671
Polymers17,5671
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)25 / 100LOW ENERGY
RepresentativeModel #1

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Components

#1: Protein KIAA0252 PROTEIN / RFT1 PLUS3 DOMAIN


Mass: 17567.150 Da / Num. of mol.: 1 / Fragment: PLUS3, RESIDUES 228-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q92541

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HNH-NOESY
131HCH-NOESY
141CNH-NOESY
151HH-NOESY
161HN(CA)CO
171HN(CA)CB
181CBCA(CO)NH
191HNCA
1101HBHA(CO)NH
1111HNCAHA
1121CCH-COSY
1131(H)CCH-TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 200 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
CYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: WATER REFINEMENT ACCORDING TO RECORD PROTOCOL
NMR ensembleConformer selection criteria: LOW ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 25

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