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- PDB-6mil: Crystal structure of AF9 YEATS domain in complex with histone H3K9bu -

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Basic information

Entry
Database: PDB / ID: 6mil
TitleCrystal structure of AF9 YEATS domain in complex with histone H3K9bu
Components
  • Histone H3K9bu
  • Protein AF-9
KeywordsTRANSCRIPTION / Epigenetic / Histone reader
Function / homology
Function and homology information


modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation ...modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / 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 / transcription elongation factor complex / 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 / negative regulation of canonical Wnt signaling pathway / 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 / chromosome / 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 / molecular adaptor activity / 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 / nucleus / membrane / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. ...YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / 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
MALONATE ION / DI(HYDROXYETHYL)ETHER / Protein AF-9 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsVann, K.R. / Klein, B.J. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AF-9
B: Histone H3K9bu
C: Protein AF-9
D: Histone H3K9bu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7236
Polymers37,5154
Non-polymers2082
Water6,161342
1
A: Protein AF-9
B: Histone H3K9bu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8643
Polymers18,7582
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-2 kcal/mol
Surface area9050 Å2
MethodPISA
2
C: Protein AF-9
D: Histone H3K9bu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8603
Polymers18,7582
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-2 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.989, 44.913, 70.804
Angle α, β, γ (deg.)90.00, 95.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-419-

HOH

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 16611.160 Da / Num. of mol.: 2 / Fragment: YEATS domain residues 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42568
#2: Protein/peptide Histone H3K9bu


Mass: 2146.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium malonate, 100 mM Bis-Tris propane pH 8.5, and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 27470 / % possible obs: 92.4 % / Redundancy: 6.1 % / Rsym value: 0.088 / Net I/σ(I): 17.2
Reflection shellResolution: 1.93→2 Å / Rsym value: 0.407

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 1.93→48.819 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2358 1818 7.27 %
Rwork0.1828 --
obs0.1866 25016 84.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→48.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 14 342 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072543
X-RAY DIFFRACTIONf_angle_d0.9313421
X-RAY DIFFRACTIONf_dihedral_angle_d22.895982
X-RAY DIFFRACTIONf_chiral_restr0.055347
X-RAY DIFFRACTIONf_plane_restr0.006448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9301-1.98230.3067740.2702966X-RAY DIFFRACTION46
1.9823-2.04060.3374910.26611159X-RAY DIFFRACTION55
2.0406-2.10640.27361100.23721357X-RAY DIFFRACTION66
2.1064-2.18170.26991320.22931631X-RAY DIFFRACTION78
2.1817-2.26910.34461320.24391722X-RAY DIFFRACTION82
2.2691-2.37240.28291490.23141906X-RAY DIFFRACTION91
2.3724-2.49740.31591530.22331949X-RAY DIFFRACTION94
2.4974-2.65390.27821520.22942013X-RAY DIFFRACTION95
2.6539-2.85880.28871600.22792021X-RAY DIFFRACTION96
2.8588-3.14640.25911600.19252057X-RAY DIFFRACTION98
3.1464-3.60160.22581650.16022100X-RAY DIFFRACTION100
3.6016-4.53710.17691680.13062127X-RAY DIFFRACTION100
4.5371-48.83490.18361720.15342190X-RAY DIFFRACTION100

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