- PDB-2k17: Solution structure of the TAF3 PHD domain in complex with a H3K4m... -
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Basic information
Entry
Database: PDB / ID: 2k17
Title
Solution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide
Components
H3K4me3 peptide
Transcription initiation factor TFIID subunit 3
Keywords
TRANSCRIPTION / PROTEIN / Alternative splicing / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information
RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / maintenance of protein location in nucleus / transcription regulator inhibitor activity / transcription factor TFIID complex / positive regulation of transcription initiation by RNA polymerase II ...RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / maintenance of protein location in nucleus / transcription regulator inhibitor activity / transcription factor TFIID complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / male germ cell nucleus / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / p53 binding / nuclear membrane / transcription by RNA polymerase II / protein heterodimerization activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function
solution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N ...solution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N terminal tail of histone H3 trimethylated at K4
Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR Details: solution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N terminal tail of histone H3 trimethylated at K4
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 1H-15N NOESY
1
2
1
3D 1H-13C NOESY
1
3
1
2D 1H-1H NOESY
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Sample preparation
Details
Contents: 0.4 mM [U-13C; U-15N] TAF3_PHD, 150 mM potassium chloride, 20 mM potassium phosphate, 0.01 mM ZnCl2, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.4mM
TAF3_PHD
[U-13C; U-15N]
1
150mM
potassiumchloride
1
20mM
potassiumphosphate
1
0.01mM
ZnCl2
1
Sample conditions
pH: 7 / Pressure: ambient / Temperature: 293 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
900
1
Bruker Avance
Bruker
AVANCE
750
2
Bruker Avance
Bruker
AVANCE
700
3
Bruker Avance
Bruker
AVANCE
600
4
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Processing
NMR software
Name
Developer
Classification
CNS
Brunger, Adams, Clore, Gros, NilgesandRead
refinement
CYANA
Guntert, MumenthalerandWuthrich
structuresolution
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
Sparky
Goddard
dataanalysis
Refinement
Method: simulated annealing / Software ordinal: 1 Details: refinement in explicit solvent using RECOORD protocol
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20
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