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- PDB-5tfp: Crystal Structure of the SETDB2 Amino Terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5tfp
TitleCrystal Structure of the SETDB2 Amino Terminal Domain
ComponentsHistone-lysine N-methyltransferase SETDB2
KeywordsTRANSFERASE / lysine methyltransferase / helical handshake motif / dimerization domain
Function / homology
Function and homology information


: / positive regulation of DNA methylation-dependent heterochromatin formation / left/right axis specification / histone H3K9 methyltransferase activity / heart looping / heterochromatin organization / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome segregation / PKMTs methylate histone lysines / chromosome ...: / positive regulation of DNA methylation-dependent heterochromatin formation / left/right axis specification / histone H3K9 methyltransferase activity / heart looping / heterochromatin organization / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome segregation / PKMTs methylate histone lysines / chromosome / mitotic cell cycle / cell division / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / 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 ...Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / 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
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Histone-lysine N-methyltransferase SETDB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKhorasanizadeh, S. / Kim, Y.
CitationJournal: To Be Published
Title: Identification of a helical dimerization domain in SETDB2 lysine methyltransferase
Authors: Khorasanizadeh, S. / Kim, Y. / Osborne, T.F. / Rastinejad, F. / Potluri, N. / Su, X. / Roqueta-Rivera, M.
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 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 SETDB2
B: Histone-lysine N-methyltransferase SETDB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,80712
Polymers14,8282
Non-polymers97910
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-36 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.474, 69.474, 120.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21B-216-

HOH

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Components

#1: Protein Histone-lysine N-methyltransferase SETDB2 / Chronic lymphocytic leukemia deletion region gene 8 protein / Lysine N-methyltransferase 1F / SET ...Chronic lymphocytic leukemia deletion region gene 8 protein / Lysine N-methyltransferase 1F / SET domain bifurcated 2


Mass: 7413.893 Da / Num. of mol.: 2 / Fragment: UNP residues 1-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB2, C13orf4, CLLD8, KMT1F / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T68, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M ammonium tartrate (pH 6.0) and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionLimit h max: 30 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / Number: 12742 / D res high: 1.97 Å / D res low: 60.166 Å / Num. obs: 12061
ReflectionResolution: 2→50 Å / Num. obs: 12089 / % possible obs: 98.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.08 / Net I/av σ(I): 22.741 / Net I/σ(I): 8.8
Reflection scaleGroup code: 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.0380.7710.8631100
2.03-2.0780.6040.914199.8
2.07-2.118.20.5670.922199.8
2.11-2.158.10.4240.95199.8
2.15-2.28.10.3980.959199.8
2.2-2.258.20.3810.962199.8
2.25-2.318.10.2890.968199.7
2.31-2.378.10.2480.978199.8
2.37-2.448.10.2170.986199.8
2.44-2.528.10.1830.985199.3
2.52-2.618.20.1490.987199.3
2.61-2.7180.1290.993199.7
2.71-2.848.10.1120.992199.3
2.84-2.9980.0940.992199.3
2.99-3.1780.0780.991199
3.17-3.4280.070.985199
3.42-3.767.90.0630.994198.3
3.76-4.317.70.0520.994198.1
4.31-5.437.60.0460.994197.5
5.43-507.20.0390.989191.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
MLPHAREphasing
PHENIX(dev-1593)refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→34.74 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.181 --
Rwork0.1619 --
obs0.1629 11469 98.8 %
Displacement parametersBiso max: 104.98 Å2 / Biso mean: 31.1359 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: LAST / Resolution: 2→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 64 52 1059
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection
Rfree0.1963 145
Rwork0.1793 -
obs-2573
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.51533.12081.28132.371.09142.1017-0.10030.2632-0.5597-0.1740.1331-0.4146-0.01870.31040.03960.17130.02430.02750.14140.01650.145150.022624.018917.7771
25.49835.79523.6137.97974.68586.57210.1087-0.13970.20110.2641-0.27570.11340.05310.01620.15780.08830.01530.0160.1170.00930.12637.623823.506926.0601
35.4302-2.644-0.61888.0086-1.52358.40540.01570.28510.2443-0.27150.28971.28020.2576-1.0469-0.24920.13060.0128-0.02410.3016-0.00040.295124.650223.91823.6125
42.82773.15970.83943.82790.88742.2909-0.21150.37330.7491-0.28870.11070.2546-0.29980.06880.16110.1527-0.0325-0.00940.16230.02670.133144.099433.672518.9581
53.49042.75250.25453.3996-1.24684.1230.2472-0.4171-0.32710.3759-0.0528-0.45690.22640.4796-0.1270.06430.0076-0.00130.2826-0.01580.196151.608326.488126.5339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resid 7 through 42 )A7 - 42
2X-RAY DIFFRACTION2chain 'A' and ( resid 43 through 64 )A43 - 64
3X-RAY DIFFRACTION3chain 'B' and ( resid 5 through 21 )B5 - 21
4X-RAY DIFFRACTION4chain 'B' and ( resid 22 through 42 )B22 - 42
5X-RAY DIFFRACTION5chain 'B' and ( resid 43 through 62 )B43 - 62

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