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- PDB-6lsd: Crystal Structure of YEATS domain of human YEATS2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6lsd
TitleCrystal Structure of YEATS domain of human YEATS2 in complex with H3K27bz peptide
Components
  • 2
  • YEATS domain-containing protein 2
KeywordsTRANSCRIPTION / YEATS domain / histone Kbz modification
Function / homology
Function and homology information


modification-dependent protein binding / ATAC complex / NuA4 histone acetyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization ...modification-dependent protein binding / ATAC complex / NuA4 histone acetyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / histone reader activity / TBP-class protein binding / 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 / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / 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 / transcription corepressor activity / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / 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 / regulation of cell cycle / chromatin remodeling / cadherin binding / 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 / membrane / nucleus
Similarity search - Function
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 / Histone-fold
Similarity search - Domain/homology
Histone H3.1 / YEATS domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, H.T. / Ren, X.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725014, 31871283, 31922016 China
National Basic Research Program of China (973 Program)2016YFA0500700 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins.
Authors: Ren, X. / Zhou, Y. / Xue, Z. / Hao, N. / Li, Y. / Guo, X. / Wang, D. / Shi, X. / Li, H.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YEATS domain-containing protein 2
B: YEATS domain-containing protein 2
C: 2
D: 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,93614
Polymers33,9794
Non-polymers95710
Water3,027168
1
A: YEATS domain-containing protein 2
hetero molecules

C: 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3706
Polymers16,9892
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
Buried area1510 Å2
ΔGint-35 kcal/mol
Surface area8860 Å2
MethodPISA
2
B: YEATS domain-containing protein 2
hetero molecules

D: 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5668
Polymers16,9892
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area1850 Å2
ΔGint-76 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.674, 89.674, 86.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422

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Components

#1: Protein YEATS domain-containing protein 2


Mass: 16087.455 Da / Num. of mol.: 2 / Fragment: YEATS domain of YEATS2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ULM3
#2: Protein/peptide 2


Mass: 902.029 Da / Num. of mol.: 2 / Fragment: histone H3 peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bis-Tris, pH 9.0, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 22927 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Χ2: 0.57 / Net I/σ(I): 6.3 / Num. measured all: 220973
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.099.10.78711320.8890.2740.8350.431100
2.09-2.12100.77211150.8690.2560.8140.423100
2.12-2.16100.64711130.9180.2140.6820.439100
2.16-2.21100.54911240.9360.1820.5790.456100
2.21-2.269.90.50911230.9480.1690.5370.44100
2.26-2.319.60.44211290.9520.150.4670.449100
2.31-2.379.40.35611290.9630.1220.3770.44100
2.37-2.4310.10.32511240.9780.1070.3430.447100
2.43-2.5100.28811300.9790.0950.3030.469100
2.5-2.589.90.24811260.9840.0820.2610.463100
2.58-2.689.60.20611300.9880.070.2180.473100
2.68-2.789.50.16611370.9920.0560.1750.502100
2.78-2.91100.12411580.9940.0410.1310.55100
2.91-3.069.90.09411260.9960.0310.10.626100
3.06-3.259.40.07311470.9970.0250.0770.67100
3.25-3.519.70.05811560.9980.020.0610.741100
3.51-3.869.70.04711670.9990.0160.050.821100
3.86-4.429.30.0411710.9990.0140.0420.902100
4.42-5.569.50.03611940.9990.0120.0380.83799.9
5.56-508.50.03412960.9990.0120.0360.825100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQL

5iql


Resolution: 2.05→44.84 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1563 6.82 %
Rwork0.1913 21359 -
obs0.1942 22922 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.39 Å2 / Biso mean: 40.0272 Å2 / Biso min: 20.24 Å2
Refinement stepCycle: final / Resolution: 2.05→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 51 168 2583
Biso mean--60.33 43.44 -
Num. residues----283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.110.30211260.235519032029
2.12-2.190.26881450.214318982043
2.19-2.280.28811380.205618972035
2.28-2.380.26981400.204919012041
2.38-2.510.33391430.210319212064
2.51-2.660.27661360.209619192055
2.67-2.870.24291660.200719032069
2.87-3.160.24981380.198419442082
3.16-3.620.21931220.179619772099
3.62-4.550.19411640.160419722136
4.56-44.840.21831450.199321242269

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