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- PDB-5wyi: The Yaf9 YEATS domain Recognizing H3K122suc Peptide -

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Basic information

Entry
Database: PDB / ID: 5wyi
TitleThe Yaf9 YEATS domain Recognizing H3K122suc Peptide
Components
  • (Yaf9) x 2
  • ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU
KeywordsTRANSCRIPTION / YEATS domain / Succinylation / Transcriptional Factor
Function / homology
Function and homology information


Swr1 complex / 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 ...Swr1 complex / 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 / 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 / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / 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 / gene expression / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA repair / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / 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
SUCCINIC ACID / Chem-SLL / Protein AF-9 homolog / Histone H3.1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Y. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
HK-RGCC7037-14G Hong Kong
CitationJournal: To Be Published
Title: The Yaf9 YEATS domain Recognizing H3K122suc Peptide
Authors: Wang, Y. / Hao, Q.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Yaf9
B: Yaf9
C: Yaf9
E: ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1526
Polymers57,7884
Non-polymers3642
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint2 kcal/mol
Surface area26030 Å2
Unit cell
Length a, b, c (Å)136.932, 136.932, 26.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-441-

HOH

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Yaf9


Mass: 18981.242 Da / Num. of mol.: 1 / Fragment: UNP residues 8-169 / Mutation: H57Y, T60K, Y76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Strain: RM11-1a / Gene: SCRG_03242
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: B3LNW5
#2: Protein Yaf9


Mass: 18924.189 Da / Num. of mol.: 2 / Fragment: UNP residues 8-169 / Mutation: H57Y, T60K, Y76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Strain: RM11-1a / Gene: SCRG_03242
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: B3LNW5

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU


Mass: 958.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

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Non-polymers , 3 types, 480 molecules

#4: Chemical ChemComp-SLL / (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid / 6-N-succinyl-L-lysine


Type: L-peptide linking / Mass: 246.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O5
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 39259 / % possible obs: 100 % / Redundancy: 5.4 % / Net I/σ(I): 13.78

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.529 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.93
RfactorNum. reflection% reflection
Rfree0.2264 1864 5.05 %
Rwork0.2013 --
obs0.2026 36911 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 23 478 3978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.29221470.25012547X-RAY DIFFRACTION95
2.0541-2.11450.26271320.22752693X-RAY DIFFRACTION99
2.1145-2.18280.26681500.23232773X-RAY DIFFRACTION100
2.1828-2.26080.24211410.22262641X-RAY DIFFRACTION100
2.2608-2.35130.25721410.21882728X-RAY DIFFRACTION100
2.3513-2.45830.24811400.22062692X-RAY DIFFRACTION100
2.4583-2.58790.23141450.22072737X-RAY DIFFRACTION100
2.5879-2.750.25631560.21592657X-RAY DIFFRACTION100
2.75-2.96230.21831240.21592763X-RAY DIFFRACTION100
2.9623-3.26020.23311540.19832722X-RAY DIFFRACTION100
3.2602-3.73170.26271290.1812714X-RAY DIFFRACTION100
3.7317-4.70030.16041510.16572669X-RAY DIFFRACTION100
4.7003-39.53660.19461540.18722711X-RAY DIFFRACTION100

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