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- PDB-6bhh: Crystal structure of SETDB1 with a modified H3 peptide -

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Basic information

Entry
Database: PDB / ID: 6bhh
TitleCrystal structure of SETDB1 with a modified H3 peptide
Components
  • Histone H3.1
  • Histone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / structural genomics / epigenetics / histone modification / mutant / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Chromatin modifying enzymes ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / 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) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / 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 / 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 / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / methylation / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : ...Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Tudor domain / Tudor domain / Post-SET domain / Post-SET domain profile. / SH3 type barrels. - #140 / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / SH3 type barrels. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsQin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2017
Title: H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1.
Authors: Jurkowska, R.Z. / Qin, S. / Kungulovski, G. / Tempel, W. / Liu, Y. / Bashtrykov, P. / Stiefelmaier, J. / Jurkowski, T.P. / Kudithipudi, S. / Weirich, S. / Tamas, R. / Wu, H. / Dombrovski, L. ...Authors: Jurkowska, R.Z. / Qin, S. / Kungulovski, G. / Tempel, W. / Liu, Y. / Bashtrykov, P. / Stiefelmaier, J. / Jurkowski, T.P. / Kudithipudi, S. / Weirich, S. / Tamas, R. / Wu, H. / Dombrovski, L. / Loppnau, P. / Reinhardt, R. / Min, J. / Jeltsch, A.
History
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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: Histone-lysine N-methyltransferase SETDB1
B: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,58830
Polymers29,3962
Non-polymers19228
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-34 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.799, 71.804, 52.544
Angle α, β, γ (deg.)90.000, 104.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase SETDB1 / ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 ...ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Lysine N-methyltransferase 1E / SET domain bifurcated 1


Mass: 27555.604 Da / Num. of mol.: 1 / Fragment: UNP residues 190-410 / Mutation: W358A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q15047, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1840.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 26 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→36.61 Å / Num. obs: 24394 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Rrim(I) all: 0.143 / Net I/σ(I): 7.9 / Num. measured all: 88658 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.863.61.179507614290.340.7291.3911.199.9
9.1-36.613.40.0416741970.9970.0260.0492795.2

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: earlier version of model from PDB entry 6BHD

6bhd


Resolution: 1.85→36.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.811 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.135
Details: PHENIX.REFINE was used for automated addition of solvent atoms to the model. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Note weak density for ...Details: PHENIX.REFINE was used for automated addition of solvent atoms to the model. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Note weak density for dimethyllysyl residues. Modeled sulfate ions may represent sulfonate moieties of partially disordered HEPES molecules.
RfactorNum. reflection% reflection
Rfree0.2374 1197 5.2 %
Rwork0.1925 --
obs0.1947 22045 99.72 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.17 Å2 / Biso mean: 23.469 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-1.44 Å2
2--0.7 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 1.85→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 36 221 1976
Biso mean--38.03 32.45 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191806
X-RAY DIFFRACTIONr_bond_other_d0.0030.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9752451
X-RAY DIFFRACTIONr_angle_other_deg0.89333933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84123.05672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70215310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2881511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_mcbond_it2.0032.236887
X-RAY DIFFRACTIONr_mcbond_other2.0022.238888
X-RAY DIFFRACTIONr_mcangle_it3.1853.3291109
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 100 -
Rwork0.305 1632 -
all-1732 -
obs--99.71 %

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