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- PDB-6mip: Crystal structure of Taf14 YEATS domain G82A mutant -

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Basic information

Entry
Database: PDB / ID: 6mip
TitleCrystal structure of Taf14 YEATS domain G82A mutant
ComponentsTranscription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / Epigenetic / Histone reader
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / transcription factor TFIIF complex / mediator complex / Ino80 complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly ...NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / transcription factor TFIIF complex / mediator complex / Ino80 complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / histone binding / transcription by RNA polymerase II / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Immunoglobulin-like ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Transcription initiation factor TFIID subunit 14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlein, B.J. / Andrews, F.H. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain.
Authors: Klein, B.J. / Vann, K.R. / Andrews, F.H. / Wang, W.W. / Zhang, J. / Zhang, Y. / Beloglazkina, A.A. / Mi, W. / Li, Y. / Li, H. / Shi, X. / Kutateladze, A.G. / Strahl, B.D. / Liu, W.R. / Kutateladze, T.G.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3012
Polymers16,1951
Non-polymers1061
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.364, 113.364, 26.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 16194.522 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-137 / Mutation: G82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 48% PEG600 with 0.2 M sodium citrate (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17536 / % possible obs: 92.8 % / Redundancy: 3.3 % / Rsym value: 0.042 / Net I/σ(I): 35.9
Reflection shellResolution: 2→2.03 Å / Rsym value: 0.092

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IOK

5iok


Resolution: 2→37.107 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.94
RfactorNum. reflection% reflection
Rfree0.2187 609 4.98 %
Rwork0.18 --
obs0.1819 12218 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→37.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 7 146 1280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071173
X-RAY DIFFRACTIONf_angle_d0.8821598
X-RAY DIFFRACTIONf_dihedral_angle_d12.952713
X-RAY DIFFRACTIONf_chiral_restr0.06179
X-RAY DIFFRACTIONf_plane_restr0.006209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.20150.2211600.18253009X-RAY DIFFRACTION96
2.2015-2.520.23471570.18853035X-RAY DIFFRACTION96
2.52-3.17470.22541570.20362958X-RAY DIFFRACTION93
3.1747-37.11340.20761350.16292607X-RAY DIFFRACTION79
Refinement TLS params.Method: refined / Origin x: -43.8938 Å / Origin y: 13.2123 Å / Origin z: 2.198 Å
111213212223313233
T0.2279 Å2-0.0525 Å2-0.0282 Å2-0.181 Å20.0443 Å2--0.1494 Å2
L1.1308 °21.3655 °20.1601 °2-4.1882 °20.1898 °2--0.4845 °2
S0.106 Å °-0.0651 Å °-0.0123 Å °0.1731 Å °-0.1942 Å °-0.4078 Å °-0.1048 Å °0.1909 Å °0.0733 Å °
Refinement TLS groupSelection details: (chain 'A' and resid -1 through 137)

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