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- PDB-3s8p: Crystal Structure of the SET Domain of Human Histone-Lysine N-Met... -

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Basic information

Entry
Database: PDB / ID: 3s8p
TitleCrystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 In Complex With S-Adenosyl-L-Methionine
ComponentsHistone-lysine N-methyltransferase SUV420H1
KeywordsTRANSFERASE / SET domain / histone methyltransferase / transcription regulation / histone lysine / SAM / methylation / nucleus / chromosome / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development ...histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development / histone methyltransferase activity / positive regulation of double-strand break repair via nonhomologous end joining / PKMTs methylate histone lysines / methylation / DNA repair / chromatin binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Histone-lysine N-methyltransferase / KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...Histone-lysine N-methyltransferase / KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase KMT5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLam, R. / Zeng, H. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2.
Authors: Wu, H. / Siarheyeva, A. / Zeng, H. / Lam, R. / Dong, A. / Wu, X.H. / Li, Y. / Schapira, M. / Vedadi, M. / Min, J.
History
DepositionMay 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SUV420H1
B: Histone-lysine N-methyltransferase SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6906
Polymers63,7622
Non-polymers9284
Water4,864270
1
A: Histone-lysine N-methyltransferase SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3453
Polymers31,8811
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3453
Polymers31,8811
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.424, 50.134, 74.839
Angle α, β, γ (deg.)100.990, 108.050, 89.760
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Histone-lysine N-methyltransferase SUV420H1 / Lysine N-methyltransferase 5B / Suppressor of variegation 4-20 homolog 1 / Su(var)4-20 homolog 1 / Suv4-20h1


Mass: 31881.123 Da / Num. of mol.: 2 / Fragment: SET domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-85, KMT5B, SUV420H1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2
References: UniProt: Q4FZB7, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M sodium formate, 0.1 M BisTris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97904 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 11, 2010 / Details: Mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 52506 / % possible obs: 97.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Χ2: 3.332 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.893.90.50934101.011196.8
1.89-1.943.90.35134761.06196.2
1.94-1.993.90.29834871.108197.1
1.99-2.053.90.2334291.158196.9
2.05-2.123.90.19334991.282197
2.12-2.193.90.15434991.323197.4
2.19-2.283.90.12335151.475197.6
2.28-2.393.90.10734681.656197.7
2.39-2.513.90.09435231.907197.9
2.51-2.673.90.08634932.355198.1
2.67-2.873.90.07235213198.4
2.87-3.163.90.06135434.452198.6
3.16-3.623.90.04835535.118198.9
3.62-4.563.90.04335536.346199.1
4.56-503.90.058353716.324199.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.85 Å / D res low: 36.86 Å / FOM acentric: 0.393 / FOM centric: 0 / Reflection acentric: 52474 / Reflection centric: 0
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.8536.86524740
ANO_10.64901.8536.86523870
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.08-36.86006300
ISO_15.78-8.080010990
ISO_14.74-5.780014410
ISO_14.12-4.740016640
ISO_13.69-4.120019080
ISO_13.37-3.690020790
ISO_13.12-3.370022480
ISO_12.92-3.120024330
ISO_12.75-2.920026030
ISO_12.61-2.750027280
ISO_12.49-2.610028450
ISO_12.39-2.490029790
ISO_12.29-2.390031240
ISO_12.21-2.290031630
ISO_12.14-2.210033660
ISO_12.07-2.140034510
ISO_12.01-2.070035030
ISO_11.95-2.010036290
ISO_11.9-1.950037650
ISO_11.85-1.90038160
ANO_18.08-36.860.3106180
ANO_15.78-8.080.295010970
ANO_14.74-5.780.336014410
ANO_14.12-4.740.369016630
ANO_13.69-4.120.407019070
ANO_13.37-3.690.417020780
ANO_13.12-3.370.453022440
ANO_12.92-3.120.486024300
ANO_12.75-2.920.528026020
ANO_12.61-2.750.584027250
ANO_12.49-2.610.642028430
ANO_12.39-2.490.706029750
ANO_12.29-2.390.778031220
ANO_12.21-2.290.828031600
ANO_12.14-2.210.875033620
ANO_12.07-2.140.904034430
ANO_12.01-2.070.936034980
ANO_11.95-2.010.958036200
ANO_11.9-1.950.969037570
ANO_11.85-1.90.987038020
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
10.256-0.1840.907SE25.141.67
29.70324.761-11.4SE24.891.56
34.57917.79-25.377SE32.541.52
4-7.663-7.7666.304SE36.651.37
517.55717.029-16.564SE34.831.3
625.50512.03-18.202SE38.051.01
75.62-6.93814.724SE44.531.31
8-15.698-11.7178.181SE54.20.89
91.78916.478-7.298SE40.270.79
108.105-8.716-3.053SE42.880.76
1121.473-6.376-3.012SE23.850.52
12-11.53518.85-7.743SE27.090.57
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.08-36.860.64206300
5.78-8.080.631010990
4.74-5.780.599014410
4.12-4.740.579016640
3.69-4.120.561019080
3.37-3.690.56020790
3.12-3.370.562022480
2.92-3.120.546024330
2.75-2.920.53026030
2.61-2.750.493027280
2.49-2.610.47028450
2.39-2.490.437029790
2.29-2.390.39031240
2.21-2.290.362031630
2.14-2.210.316033660
2.07-2.140.282034510
2.01-2.070.245035030
1.95-2.010.224036290
1.9-1.950.202037650
1.85-1.90.174038160
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 52473
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.62-10058.90.868522
6.54-8.6254.80.92680
5.48-6.5454.80.936845
4.81-5.4851.20.938987
4.33-4.8152.80.9431114
3.98-4.3353.70.951217
3.7-3.9853.70.9431309
3.47-3.754.50.9351415
3.28-3.4754.30.9361449
3.12-3.2855.60.9221566
2.98-3.1257.90.9161655
2.85-2.9855.70.9151705
2.74-2.8555.90.9111800
2.65-2.7456.80.9091842
2.56-2.6557.90.9011907
2.48-2.56580.9031996
2.41-2.48590.9032021
2.34-2.4163.90.9092069
2.28-2.3463.10.9072140
2.22-2.2864.50.9062216
2.17-2.2266.30.9072258
2.12-2.1768.40.9042287
2.08-2.1269.40.912350
2.03-2.0872.80.9092395
1.99-2.0373.20.92451
1.95-1.9976.90.92481
1.92-1.9576.10.8982504
1.88-1.9279.70.8722620
1.85-1.8881.50.7992672

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→33.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 4.654 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 2672 5.1 %RANDOM
Rwork0.187 ---
obs0.1882 52470 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 123.67 Å2 / Biso mean: 34.4083 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å20.02 Å2
2---0.06 Å20.04 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 56 270 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223849
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9675188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86724.55189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04815667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4081522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022933
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 213 -
Rwork0.246 3600 -
all-3813 -
obs--96.56 %
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)
11.252-0.3530.27350.6402-0.27110.71290.0126-0.17880.04270.00050.026-0.00090.0033-0.0154-0.03850.0327-0.0084-0.00090.0315-0.00170.01545.45844.27.46
20.9920.27040.32680.76950.63761.06060.01210.12070.0337-0.02130.006-0.0267-0.0520.0116-0.01810.0330.00760.00680.01660.00640.01055.1718.926-18.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 334
2X-RAY DIFFRACTION2B71 - 333

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