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- PDB-5j9s: ENL YEATS in complex with histone H3 acetylation at K27 -

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Basic information

Entry
Database: PDB / ID: 5j9s
TitleENL YEATS in complex with histone H3 acetylation at K27
Components
  • H3K27ac peptide from Histone H3.1
  • Protein ENL
KeywordsTRANSCRIPTION / Complex / ENL YEATS / histone acetyllysine / H3K27
Function / homology
Function and homology information


Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / transcription elongation factor complex / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / lysine-acetylated histone binding / 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 / fibrillar center / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsLi, Y. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foudation pf China91519304 China
CitationJournal: Nature / Year: 2017
Title: ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia
Authors: Wan, L. / Wen, H. / Li, Y. / Lyu, J. / Xi, Y. / Hoshii, T. / Joseph, J.K. / Wang, X. / Loh, Y.E. / Erb, M.A. / Souza, A.L. / Bradner, J.E. / Shen, L. / Li, W. / Li, H. / Allis, C.D. / Armstrong, S.A. / Shi, X.
History
DepositionApr 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Nov 8, 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
B: H3K27ac peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3156
Polymers20,9312
Non-polymers3844
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-45 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.979, 104.979, 45.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18312.080 Da / Num. of mol.: 1 / Fragment: UNP residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q03111
#2: Protein/peptide H3K27ac peptide from Histone H3.1


Mass: 2619.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.43 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M K/Na Tartrate, 0.1M Sodium citrate tribasic dihydrate, pH 5.6, 2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8062 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.64 Å2 / Rmerge(I) obs: 0.234 / Χ2: 1.521 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.7-2.756.50.8091.1821100
2.75-2.86.40.7571.234199.8
2.8-2.856.50.6841.3441100
2.85-2.916.60.5561.263199.7
2.91-2.976.40.5261.279199.5
2.97-3.046.50.4381.3311100
3.04-3.126.50.3821.2031100
3.12-3.26.40.3221.284199.8
3.2-3.36.50.2741.4311100
3.3-3.46.40.2711.381100
3.4-3.526.40.2121.416199.5
3.52-3.666.50.1741.7051100
3.66-3.836.40.171.588199.8
3.83-4.036.40.1781.6591100
4.03-4.296.30.1641.797199.8
4.29-4.626.20.1512.3631100
4.62-5.086.10.1422.083199.8
5.08-5.816.20.1851.713199.8
5.81-7.3260.1751.454199.8
7.32-5060.0991.748197.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.702→40.422 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 771 9.58 %
Rwork0.1848 7279 -
obs0.1872 8050 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.36 Å2 / Biso mean: 23.1289 Å2 / Biso min: 1.71 Å2
Refinement stepCycle: final / Resolution: 2.702→40.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 20 51 1364
Biso mean--42.4 22.91 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031350
X-RAY DIFFRACTIONf_angle_d0.6111826
X-RAY DIFFRACTIONf_chiral_restr0.045183
X-RAY DIFFRACTIONf_plane_restr0.003236
X-RAY DIFFRACTIONf_dihedral_angle_d21.161793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7016-2.87080.32061300.250911961326100
2.8708-3.09240.26111380.224511831321100
3.0924-3.40340.20761210.189412051326100
3.4034-3.89560.18961350.15412091344100
3.8956-4.90670.16371290.140712101339100
4.9067-40.42660.20041180.21121276139499

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