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- PDB-5tdw: Set3 PHD finger in complex with histone H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 5tdw
TitleSet3 PHD finger in complex with histone H3K4me3
Components
  • SET domain-containing protein 3
  • histone H3K4me3
KeywordsTRANSCRIPTION / Transcription / epigenetics / methylation / histone
Function / homologyZinc finger, PHD-type, conserved site / Zinc finger, PHD-finger / PKMTs methylate histone lysines / HDACs deacetylate histones / Histone H3/CENP-A / SET domain / Zinc finger, PHD-type / Histone H2A/H2B/H3 / Histone-fold / Zinc finger, FYVE/PHD-type ...Zinc finger, PHD-type, conserved site / Zinc finger, PHD-finger / PKMTs methylate histone lysines / HDACs deacetylate histones / Histone H3/CENP-A / SET domain / Zinc finger, PHD-type / Histone H2A/H2B/H3 / Histone-fold / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Senescence-Associated Secretory Phenotype (SASP) / Core histone H2A/H2B/H3/H4 / Oxidative Stress Induced Senescence / PHD-finger / Histone H3 signature 1. / Histone H3 signature 2. / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / SET domain profile. / Interleukin-7 signaling / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDMs demethylate histones / HATs acetylate histones / RMTs methylate histone arginines / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / Amyloid fiber formation / Meiotic recombination / Estrogen-dependent gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RNA Polymerase I Chain Elongation / RNA Polymerase I Promoter Opening / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation by small RNAs / DNA methylation / B-WICH complex positively regulates rRNA expression / NoRC negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / Rpd3L-Expanded complex / Set3 complex / negative regulation of meiotic nuclear division / histone deacetylation / interleukin-7-mediated signaling pathway / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / regulation of gene silencing by miRNA / chromatin silencing at rDNA / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / methylated histone binding / regulation of gene silencing / regulation of megakaryocyte differentiation / meiotic cell cycle / nucleosome / nucleosome assembly / protein heterotetramerization / chromatin organization / cadherin binding / blood coagulation / regulation of transcription, DNA-templated / cellular protein metabolic process / protein heterodimerization activity / protein-containing complex / extracellular exosome / membrane / nucleoplasm / extracellular region / metal ion binding / nucleus / SET domain-containing protein 3 / Histone H3.1
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.7 Å resolution
AuthorsAndrews, F.H. / Ali, M. / Kutateladze, T.G.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Insight into Recognition of Methylated Histone H3K4 by Set3.
Authors: Gatchalian, J. / Ali, M. / Andrews, F.H. / Zhang, Y. / Barrett, A.S. / Kutateladze, T.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2016 / Release: Oct 19, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 19, 2016Structure modelrepositoryInitial release
1.1Jun 28, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SET domain-containing protein 3
B: histone H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3575
Polyers9,2032
Non-polymers1543
Water3,693205
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1150
ΔGint (kcal/M)-15
Surface area (Å2)5500
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)25.870, 43.680, 85.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 2 21 21

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Components

#1: Protein/peptide SET domain-containing protein 3


Mass: 7909.953 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SET3, YKR029C / Production host: Escherichia coli (E. coli) / References: UniProt: P36124
#2: Protein/peptide histone H3K4me3


Mass: 1293.516 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Formula: H2O / Water

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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: 2.61 / Density percent sol: 52.89 %
Crystal growTemp: 273 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Collection date: Mar 2, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.7 Å / D resolution low: 42.54 Å / Number obs: 11089 / NetI over sigmaI: 14 / Redundancy: 26.5 % / Percent possible obs: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefineOverall SU ML: 0.14 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 17.61
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.1991 / R factor R work: 0.1645 / R factor obs: 0.1662 / Highest resolution: 1.7 Å / Lowest resolution: 42.53 Å / Number reflection R free: 555 / Number reflection obs: 11089 / Percent reflection R free: 5 / Percent reflection obs: 99.12
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 42.53 Å
Number of atoms included #LASTProtein: 636 / Nucleic acid: 0 / Ligand: 3 / Solvent: 205 / Total: 844
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008655
X-RAY DIFFRACTIONf_angle_d1.134884
X-RAY DIFFRACTIONf_dihedral_angle_d14.207251
X-RAY DIFFRACTIONf_chiral_restr0.05897
X-RAY DIFFRACTIONf_plane_restr0.005117
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.70000.23280.17581.8711134254898.00
1.87110.21890.16652.1419137258699.00
2.14190.19800.17182.6985137262299.00
2.69850.17900.155142.54331472778100.00

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