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- PDB-6bpi: Crystal structure of SETDB1 Tudor domain with aryl triazole fragm... -

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Basic information

Entry
Database: PDB / ID: 6bpi
TitleCrystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates
Components
  • Histone-lysine N-methyltransferase SETDB1
  • MLY-SER-THR-E2G
KeywordsTRANSFERASE / SETDB1 Tudor / fragment hits / epigenetics / methyl lysine reader / Structural Genomics / 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 / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / promoter-specific chromatin binding / PKMTs methylate histone lysines ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromosome / methylation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / 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 / Pre-SET domain ...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 domain / Pre-SET motif / 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 superfamily / SET domain / SET domain profile. / SET domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.64 Å
AuthorsMADER, P. / Mendoza-Sanchez, R. / DONG, A. / DOBROVETSKY, E. / IQBAL, A. / CORLESS, V. / TEMPEL, W. / LIEW, S.K. / SMIL, D. / DELA SENA, C.C. ...MADER, P. / Mendoza-Sanchez, R. / DONG, A. / DOBROVETSKY, E. / IQBAL, A. / CORLESS, V. / TEMPEL, W. / LIEW, S.K. / SMIL, D. / DELA SENA, C.C. / KENNEDY, S. / DIAZ, D.B. / SCHAPIRA, M. / VEDADI, M. / BROWN, P.J. / Santhakumar, V. / FRYE, S. / Bountra, C. / Edwards, A.M. / YUDIN, A.K. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates
Authors: MADER, P. / Mendoza-Sanchez, R. / DONG, A. / DOBROVETSKY, E. / IQBAL, A. / CORLESS, V. / TEMPEL, W. / LIEW, S.K. / SMIL, D. / DELA SENA, C.C. / KENNEDY, S. / DIAZ, D.B. / SCHAPIRA, M. / ...Authors: MADER, P. / Mendoza-Sanchez, R. / DONG, A. / DOBROVETSKY, E. / IQBAL, A. / CORLESS, V. / TEMPEL, W. / LIEW, S.K. / SMIL, D. / DELA SENA, C.C. / KENNEDY, S. / DIAZ, D.B. / SCHAPIRA, M. / VEDADI, M. / BROWN, P.J. / Santhakumar, V. / FRYE, S. / Bountra, C. / Edwards, A.M. / YUDIN, A.K. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionNov 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETDB1
B: MLY-SER-THR-E2G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,13512
Polymers25,5652
Non-polymers57010
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-40 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.731, 63.756, 69.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 24887.756 Da / Num. of mol.: 1 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: pET28a-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q15047, histone-lysine N-methyltransferase
#2: Protein/peptide MLY-SER-THR-E2G


Mass: 676.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 166 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.34 Å3/Da / Density % sol: 47.48 % / Mosaicity: 0.678 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3350, 0.2M LiSO4, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 30573 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.013 / Rrim(I) all: 0.036 / Χ2: 0.84 / Net I/σ(I): 15.9 / Num. measured all: 227487
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.6750.64514860.80.3050.7170.78899.1
1.67-1.76.80.5415160.8960.2210.5850.899.9
1.7-1.737.40.43815020.930.1730.4720.784100
1.73-1.777.50.37615090.9380.1480.4040.777100
1.77-1.817.50.30814860.9610.120.3310.773100
1.81-1.857.50.21915180.9810.0850.2350.799100
1.85-1.897.60.18115160.9870.070.1940.816100
1.89-1.947.60.1415060.9920.0540.150.832100
1.94-27.60.1115070.9950.0430.1190.845100
2-2.077.70.0915110.9960.0350.0970.865100
2.07-2.147.70.07115280.9980.0270.0770.884100
2.14-2.237.70.06315150.9980.0240.0670.901100
2.23-2.337.70.05615230.9980.0210.060.946100
2.33-2.457.80.04715300.9990.0180.0510.895100
2.45-2.67.80.0415320.9990.0150.0420.85100
2.6-2.87.80.03215390.9990.0120.0350.82100
2.8-3.097.80.026154110.010.0280.816100
3.09-3.537.80.021156510.0080.0230.801100
3.53-4.457.70.019157510.0070.0210.89100
4.45-5070.02166810.0080.0220.8898.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.64→47.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.793 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19939 917 3 %RANDOM
Rwork0.18785 ---
obs0.18822 29574 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2---0.71 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.64→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 35 156 1906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191959
X-RAY DIFFRACTIONr_bond_other_d0.0020.021790
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.952673
X-RAY DIFFRACTIONr_angle_other_deg0.87634138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55422.584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71515326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1281516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02455
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5332.385916
X-RAY DIFFRACTIONr_mcbond_other1.5322.385917
X-RAY DIFFRACTIONr_mcangle_it2.5013.5651163
X-RAY DIFFRACTIONr_mcangle_other2.53.5651164
X-RAY DIFFRACTIONr_scbond_it1.9242.6441043
X-RAY DIFFRACTIONr_scbond_other1.9242.6441044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0993.8911507
X-RAY DIFFRACTIONr_long_range_B_refined5.45427.6852177
X-RAY DIFFRACTIONr_long_range_B_other5.44927.6682177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 59 -
Rwork0.358 2158 -
obs--99.46 %

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