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

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Basic information

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


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 dimethyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K9 trimethyltransferase activity / heterochromatin organization / transposable element silencing by heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9 monomethyltransferase activity / histone H3K14ac reader activity / DNA methylation-dependent constitutive heterochromatin formation ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 dimethyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K9 trimethyltransferase activity / heterochromatin organization / transposable element silencing by heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9 monomethyltransferase activity / histone H3K14ac reader activity / DNA methylation-dependent constitutive heterochromatin formation / histone H3K9me2/3 reader activity / histone H3 methyltransferase activity / 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) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / epigenetic regulation of gene expression / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / nucleosome assembly / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dengue Virus-Host Interactions / Senescence-Associated Secretory Phenotype (SASP) / methylation / heterochromatin formation / Oxidative Stress Induced Senescence / chromatin organization / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / chromatin binding / chromatin / protein-containing complex / DNA binding / DNA-templated transcription / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / membrane / nucleus / 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 profile. / SET domain superfamily / SET domain / SH3 type barrels. / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsQin, S. / Tempel, W. / Dong, A. / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,48442
Polymers29,4842
Non-polymers040
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.709, 72.363, 52.501
Angle α, β, γ (deg.)90.000, 104.750, 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: 1813.113 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.: 40 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 47.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 20% PEG5000 MME, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.4→41.56 Å / Num. obs: 53270 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 19.9 / Num. measured all: 196395 / 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
1.4-1.422.80.826683824360.5910.5941.0251.493.1
7.67-41.563.40.01911793440.9990.0120.02268.998.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: earlier version of coordinates of nearly isomorphous crystal structure (see PDB entry 6BHE)

6bhe


Resolution: 1.45→41.56 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.283 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: We thank Aiping Dong for collection of diffraction data. Water sites were picked with PHENIX. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. ...Details: We thank Aiping Dong for collection of diffraction data. Water sites were picked with PHENIX. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Uninterpreted density in the aromatic cage of Tudor domain three may have arisen from the K9 side chain of bound histone peptide or from the R384 side chain of SETDB1.
RfactorNum. reflection% reflection
Rfree0.1761 2428 5 %
Rwork0.133 --
obs0.1352 45714 99.65 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.44 Å2 / Biso mean: 20.631 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.42 Å2
2---0.29 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.45→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 40 223 2013
Biso mean--36.09 33.54 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021857
X-RAY DIFFRACTIONr_bond_other_d0.0030.021735
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9662529
X-RAY DIFFRACTIONr_angle_other_deg0.99634024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70623.19472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.37215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212043
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
X-RAY DIFFRACTIONr_mcbond_it2.651.849916
X-RAY DIFFRACTIONr_mcbond_other2.5631.845915
X-RAY DIFFRACTIONr_mcangle_it3.0492.781145
X-RAY DIFFRACTIONr_rigid_bond_restr2.18533592
X-RAY DIFFRACTIONr_sphericity_free26.8595148
X-RAY DIFFRACTIONr_sphericity_bonded13.05953656
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 182 -
Rwork0.204 3337 -
all-3519 -
obs--99.91 %

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