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- PDB-2kiq: Solution structure of the FF Domain 2 of human transcription elon... -

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Basic information

Entry
Database: PDB / ID: 2kiq
TitleSolution structure of the FF Domain 2 of human transcription elongation factor CA150
ComponentsTranscription elongation regulator 1
KeywordsTRANSCRIPTION REGULATOR / Human transcription elongation factor CA150 / RNA polymerase II C-terminal domain interacting protein / FF domain / Residual dipolar coupling / Activator / Alternative splicing / Coiled coil / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity ...transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
FF domain / Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...FF domain / Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription elongation regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / GLOBAL FOLD COMPUTATION BASED ON EXACT SOLUTIONS FROM RDCS, NOE ASSIGNMENT BASED ON HAUSDORFF-BASED PATTERN MATCHING, ENERGY-MINIMIZATION
Model detailslowest energy, model 1
AuthorsZeng, J. / Boyles, J. / Tripathy, C. / Yan, A. / Zhou, P. / Donald, B.R.
CitationJournal: J.Biomol.Nmr / Year: 2009
Title: High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Authors: Zeng, J. / Boyles, J. / Tripathy, C. / Wang, L. / Yan, A. / Zhou, P. / Donald, B.R.
History
DepositionMay 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 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: Transcription elongation regulator 1


Theoretical massNumber of molelcules
Total (without water)7,3161
Polymers7,3161
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 / 50structures with the lowest energy and acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription elongation regulator 1 / / TATA box-binding protein-associated factor 2S / Transcription factor CA150


Mass: 7315.560 Da / Num. of mol.: 1 / Fragment: UNP residues 724-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCERG1, CA150, TAF2S / Plasmid: pET15b-modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14776

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D HNCO
1623D (H)CCH-TOCSY
1713D HN(CO)CA
1813D HN(COCA)CB
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] CA150 FF2-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] CA150 FF2-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCA150 FF2-1[U-100% 15N]1
1 mMCA150 FF2-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 25 / pH: 7.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
RDC-PANDA1RDC-PANDA (AUTHORS: J. ZENG, J. BOYLES, C. TRIPATHY, L. WANG, A. YAN, P. ZHOU AND B.R. DONALD)noe assignment
RDC-PANDA1RDC-PANDA (AUTHORS: J. ZENG, J. BOYLES, C. TRIPATHY, L. WANG, A. YAN, P. ZHOU AND B.R. DONALD)exact solutions for backbone conformations from rdcs
RDC-PANDA1RDC-PANDA (AUTHORS: J. ZENG, J. BOYLES, C. TRIPATHY, L. WANG, A. YAN, P. ZHOU AND B.R. DONALD)packing secondary structure elements using sparse noes, and computing global fold
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
RefinementMethod: GLOBAL FOLD COMPUTATION BASED ON EXACT SOLUTIONS FROM RDCS, NOE ASSIGNMENT BASED ON HAUSDORFF-BASED PATTERN MATCHING, ENERGY-MINIMIZATION
Software ordinal: 1
Details: 1. ORIENTATIONS AND CONFORMATIONS OF SECONDARY STRUCTURE ELEMENTS WERE CALCULATED USING THE RDC-EXACT MODULE, WHICH EXACTLY SOLVES A SYSTEM OF QUARTIC RDC EQUATIONS AND COMPUTES THE GLOBAL ...Details: 1. ORIENTATIONS AND CONFORMATIONS OF SECONDARY STRUCTURE ELEMENTS WERE CALCULATED USING THE RDC-EXACT MODULE, WHICH EXACTLY SOLVES A SYSTEM OF QUARTIC RDC EQUATIONS AND COMPUTES THE GLOBAL OPTIMAL SOLUTIONS OF BACKBONE DIHEDRAL ANGLES. 2. THE PACKER MODULE WAS USED TO DETERMINE THE TRANSLATIONS BETWEEN SECONDARY STRUCTURE ELEMENTS USING A SPARSE SET OF NOE DISTANCE RESTRAINTS. THE HANA MODULE WAS USED TO COMPUTE NOE ASSIGNMENTS BASED ON A HAUSDORFF-BASED PATTERN MATCHING TECHNIQUE. THE STRUCTURES WERE REFINED AGAINST RESIDUAL DIPOLAR COUPLINGS USING XPLOR-NIH AND A WATER-REFINEMENT PROTOCOL.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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