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- PDB-6min: Crystal structure of Taf14 YEATS domain G82A mutant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6min
TitleCrystal structure of Taf14 YEATS domain G82A mutant in complex with histone H3K9cr
Components
  • Histone H3K9cr
  • Transcription 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 / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / histone binding / gene expression / Estrogen-dependent gene expression / transcription by RNA polymerase II / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / 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 / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
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. ...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 domain / 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: 1.9 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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 H3K9cr


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers17,0812
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-1 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.446, 113.446, 26.392
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: Protein/peptide Histone H3K9cr


Mass: 885.986 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.: 155 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 44% 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: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→37.14 Å / Num. obs: 15267 / % possible obs: 96.7 % / Redundancy: 4.3 % / Rsym value: 0.048 / Net I/σ(I): 40
Reflection shellResolution: 1.9→1.93 Å / Rsym value: 0.164

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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: 1.9→37.134 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2556 1454 9.94 %
Rwork0.2018 --
obs0.207 14635 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 155 1337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061212
X-RAY DIFFRACTIONf_angle_d0.8721648
X-RAY DIFFRACTIONf_dihedral_angle_d18.546459
X-RAY DIFFRACTIONf_chiral_restr0.058185
X-RAY DIFFRACTIONf_plane_restr0.006216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.27341310.26261208X-RAY DIFFRACTION87
1.9679-2.04670.29781460.23381329X-RAY DIFFRACTION93
2.0467-2.13980.28111480.22871367X-RAY DIFFRACTION99
2.1398-2.25260.28061520.23721388X-RAY DIFFRACTION99
2.2526-2.39380.26021550.23451380X-RAY DIFFRACTION97
2.3938-2.57850.29671490.22421314X-RAY DIFFRACTION94
2.5785-2.83790.28891420.22951283X-RAY DIFFRACTION91
2.8379-3.24840.27111380.20741278X-RAY DIFFRACTION89
3.2484-4.09180.22641420.16861297X-RAY DIFFRACTION91
4.0918-37.1410.21791510.16851337X-RAY DIFFRACTION89

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