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- PDB-6mio: Crystal structure of Taf14 YEATS domain in complex with histone H3K9pr -

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Basic information

Entry
Database: PDB / ID: 6mio
TitleCrystal structure of Taf14 YEATS domain in complex with histone H3K9pr
Components
  • Histone H3K9pr
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / Epigenetic / Histone reader
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / transcription factor TFIIF complex / mediator complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Chromatin modifying enzymes ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / transcription factor TFIIF complex / mediator complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA polymerase II preinitiation complex assembly / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription by RNA polymerase II / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 14 / Histone H3.1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKlein, B.J. / Andrews, F.H. / Vann, K.R. / 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
B: Histone H3K9pr


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers17,0542
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-1 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.211, 113.211, 26.237
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: 16180.497 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-137
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: Protein/peptide Histone H3K9pr


Mass: 873.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 46% PEG600 (v/v) and 0.2 M citric acid (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: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→37.06 Å / Num. obs: 16550 / % possible obs: 97.8 % / Redundancy: 4.3 % / Rsym value: 0.054 / Net I/σ(I): 51.8
Reflection shellResolution: 2→2.03 Å / Rsym value: 0.15

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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: 1.85→37.057 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2319 1601 10.04 %
Rwork0.1823 --
obs0.1873 15951 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 180 1379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071243
X-RAY DIFFRACTIONf_angle_d0.9141694
X-RAY DIFFRACTIONf_dihedral_angle_d17.814477
X-RAY DIFFRACTIONf_chiral_restr0.06189
X-RAY DIFFRACTIONf_plane_restr0.006223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8497-1.90940.28651360.2361144X-RAY DIFFRACTION85
1.9094-1.97770.27451290.23111193X-RAY DIFFRACTION87
1.9777-2.05690.27671420.20551251X-RAY DIFFRACTION91
2.0569-2.15050.27311450.2061279X-RAY DIFFRACTION94
2.1505-2.26380.26461420.21091314X-RAY DIFFRACTION97
2.2638-2.40560.23061560.20121348X-RAY DIFFRACTION97
2.4056-2.59130.241470.19031328X-RAY DIFFRACTION96
2.5913-2.8520.2581410.20371334X-RAY DIFFRACTION97
2.852-3.26450.24161520.19071362X-RAY DIFFRACTION97
3.2645-4.11210.17871500.1521377X-RAY DIFFRACTION99
4.1121-37.06440.21781610.15371420X-RAY DIFFRACTION96

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