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

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Basic information

Entry
Database: PDB / ID: 6bhe
TitleCrystal structure of SETDB1 with a modified H3 peptide
Components
  • Histone H3.1
  • Histone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / structural genomics / epigenetics / histone modification / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.0Dec 6, 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


Theoretical massNumber of molelcules
Total (without water)29,52638
Polymers29,5262
Non-polymers036
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.051, 71.372, 52.055
Angle α, β, γ (deg.)90.000, 104.230, 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: 27670.734 Da / Num. of mol.: 1 / Fragment: UNP residues 190-410
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: 1855.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.33→41.2 Å / Num. obs: 60118 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 15.3 / Num. measured all: 221167 / 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
1.33-1.353.61.1531074229640.4950.7031.3541.299.9
7.28-41.23.30.02111753510.9990.0140.02554.191.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DLM

3dlm


Resolution: 1.35→35.69 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.923 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflection
Rfree0.1725 2872 5 %
Rwork0.1345 --
obs0.1364 54617 99.76 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.19 Å2 / Biso mean: 19.566 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0.29 Å2
2---0.03 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.35→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 36 149 1976
Biso mean--37.48 31.55 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021956
X-RAY DIFFRACTIONr_bond_other_d0.0060.021842
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9692682
X-RAY DIFFRACTIONr_angle_other_deg1.01734275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81523.03879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54915337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4221512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02421
X-RAY DIFFRACTIONr_mcbond_it2.4691.747947
X-RAY DIFFRACTIONr_mcbond_other2.4721.744946
X-RAY DIFFRACTIONr_mcangle_it2.8872.6251189
X-RAY DIFFRACTIONr_rigid_bond_restr2.15333797
X-RAY DIFFRACTIONr_sphericity_free26.8155111
X-RAY DIFFRACTIONr_sphericity_bonded11.97653808
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 211 -
Rwork0.267 4034 -
all-4245 -
obs--99.88 %

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