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- PDB-3qrl: Crystal Structure of the Taf14 YEATS domain -

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Basic information

Entry
Database: PDB / ID: 3qrl
TitleCrystal Structure of the Taf14 YEATS domain
ComponentsTranscription initiation factor TFIID subunit 14
KeywordsNUCLEAR PROTEIN / YEATS domain / Ig fold / Nucleus
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / mediator complex / transcription factor TFIIF 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 / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / mediator complex / transcription factor TFIIF 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Transcription initiation factor TFIID subunit 14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSimpson, P.J. / Warren, A.J.
CitationJournal: To be Published
Title: Crystal structure of the Taf14 YEATS domain
Authors: Simpson, P.J. / Warren, A.J.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,2012
Polymers16,0511
Non-polymers1501
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.019, 113.019, 26.329
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: 16051.319 Da / Num. of mol.: 1 / Fragment: YEATS Domain (UNP Residues 1-137)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: Y5563 / Gene: ANC1, CST10, SWP29, TAF14, TAF30, TFG3, YPL129W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P35189
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 42.5% (v/v) PEG-600, 100 mM Sodium Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2009 / Details: Mirrors
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→32.626 Å / Num. obs: 21602 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 24.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3130 / Rsym value: 0.408 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
autoSHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.626 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.36 / SU ML: 0.076 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 1104 5.1 %RANDOM
Rwork0.18757 ---
obs0.18988 20494 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.688 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å2-0.98 Å20 Å2
2---1.96 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 10 139 1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221178
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9791606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47824.46456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32615204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.687157
X-RAY DIFFRACTIONr_chiral_restr0.1270.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.022897
X-RAY DIFFRACTIONr_mcbond_it2.1911.5701
X-RAY DIFFRACTIONr_mcangle_it3.39321162
X-RAY DIFFRACTIONr_scbond_it4.9283477
X-RAY DIFFRACTIONr_scangle_it8.0914.5441
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 74 -
Rwork0.346 1514 -
obs-1514 99.94 %
Refinement TLS params.Method: refined / Origin x: 45.8028 Å / Origin y: 53.3179 Å / Origin z: 1.8264 Å
111213212223313233
T0.0677 Å2-0.0044 Å2-0.0316 Å2-0.1373 Å20.0234 Å2--0.0829 Å2
L5.515 °2-1.1602 °2-0.4711 °2-1.2033 °2-0.0714 °2--0.1726 °2
S-0.036 Å °0.106 Å °0.3224 Å °0.0645 Å °-0.0011 Å °-0.1772 Å °-0.081 Å °0.0342 Å °0.037 Å °

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