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- PDB-5xnv: Crystal structure of YEATS2 YEATS bound to H3K27ac peptide -

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Basic information

Entry
Database: PDB / ID: 5xnv
TitleCrystal structure of YEATS2 YEATS bound to H3K27ac peptide
Components
  • ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
  • YEATS domain-containing protein 2
KeywordsPROTEIN BINDING/PEPTIDE / epigenetics / histone reader / histone acetylation / protein complex / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


modification-dependent protein binding / ATAC complex / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / histone reader activity / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling ...modification-dependent protein binding / ATAC complex / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / histone reader activity / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / TBP-class protein binding / 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 / mitotic spindle / structural constituent of chromatin / transcription corepressor activity / 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) / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
: / Three-helical bundle domain / YEATS domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. ...: / Three-helical bundle domain / 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
AMMONIUM ION / Histone H3.1 / YEATS domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.696 Å
AuthorsLi, H.T. / Guan, H.P. / Zhao, D.
Funding support China, 2items
OrganizationGrant numberCountry
Major State Basic Research Development Program2015CB910503 China
National Natural Science Foundation of China91519304 China
CitationJournal: Nat Commun / Year: 2017
Title: YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer.
Authors: Mi, W. / Guan, H. / Lyu, J. / Zhao, D. / Xi, Y. / Jiang, S. / Andrews, F.H. / Wang, X. / Gagea, M. / Wen, H. / Tora, L. / Dent, S.Y.R. / Kutateladze, T.G. / Li, W. / Li, H. / Shi, X.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YEATS domain-containing protein 2
B: ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7226
Polymers16,6322
Non-polymers904
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-4 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.826, 72.826, 125.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-405-

CL

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Components

#1: Protein YEATS domain-containing protein 2


Mass: 15818.110 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 201-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9ULM3
#2: Protein/peptide ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA


Mass: 813.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1M CAPS, pH 10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.696→39.8 Å / Num. obs: 4915 / % possible obs: 99.5 % / Redundancy: 3.8 % / Net I/σ(I): 17.53

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.696→39.773 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 29.24
RfactorNum. reflection% reflection
Rfree0.266 465 9.46 %
Rwork0.2242 --
obs0.2285 4914 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.696→39.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 5 13 1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011201
X-RAY DIFFRACTIONf_angle_d1.2681624
X-RAY DIFFRACTIONf_dihedral_angle_d14.87454
X-RAY DIFFRACTIONf_chiral_restr0.054173
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6958-3.08570.30321340.24791437X-RAY DIFFRACTION99
3.0857-3.88720.23951540.21611467X-RAY DIFFRACTION100
3.8872-39.77740.27111770.22181545X-RAY DIFFRACTION100

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