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- PDB-6p0r: Methyltransferase domain of human suppressor of variegation 3-9 h... -

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Basic information

Entry
Database: PDB / ID: 6p0r
TitleMethyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor
ComponentsHistone-lysine N-methyltransferase SUV39H2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Methyltransferase domain / SUV39H2 / OTS186935 / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / epigenetic programming in the zygotic pronuclei / S-adenosyl-L-methionine binding / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / ubiquitin-like ligase-substrate adaptor activity / chromosome, centromeric region / PKMTs methylate histone lysines ...[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / epigenetic programming in the zygotic pronuclei / S-adenosyl-L-methionine binding / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / ubiquitin-like ligase-substrate adaptor activity / chromosome, centromeric region / PKMTs methylate histone lysines / circadian rhythm / methylation / chromatin organization / cellular response to hypoxia / cell differentiation / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-NM4 / Histone-lysine N-methyltransferase SUV39H2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHalabelian, L. / Dong, A. / Zeng, H. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor
Authors: Halabelian, L. / Dong, A. / Zeng, H. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SUV39H2
B: Histone-lysine N-methyltransferase SUV39H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,36413
Polymers67,8472
Non-polymers1,51711
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.701, 63.388, 65.616
Angle α, β, γ (deg.)90.000, 113.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histone-lysine N-methyltransferase SUV39H2 / Histone H3-K9 methyltransferase 2 / H3-K9-HMTase 2 / Lysine N-methyltransferase 1B / Suppressor of ...Histone H3-K9 methyltransferase 2 / H3-K9-HMTase 2 / Lysine N-methyltransferase 1B / Suppressor of variegation 3-9 homolog 2 / Su(var)3-9 homolog 2


Mass: 33923.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUV39H2, KMT1B / Plasmid: pET15-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H5I1, histone-lysine N-methyltransferase
#2: Chemical ChemComp-NM4 / (3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine


Mass: 463.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C25H26ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.07 Å3/Da / Density % sol: 40.49 % / Mosaicity: 1.839 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M NH4Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21217 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.088 / Rrim(I) all: 0.166 / Χ2: 1.682 / Net I/σ(I): 6.9 / Num. measured all: 71065
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.20.77810780.7030.5030.9310.70698.4
2.44-2.493.30.75710450.670.4860.9040.69298.4
2.49-2.533.40.74310610.6490.4730.8850.7298.8
2.53-2.593.30.65110570.6720.4140.7760.73499.2
2.59-2.643.30.57310660.7170.3680.6840.83398.3
2.64-2.73.30.5410570.7390.3450.6440.92199
2.7-2.773.30.46110610.8150.2960.5510.85698.7
2.77-2.853.20.37310830.8480.240.4460.89498.1
2.85-2.933.10.31210230.870.2060.3771.04696.5
2.93-3.022.90.2429850.9160.1630.2931.2192.5
3.02-3.1330.23910060.9370.1570.2881.16592.8
3.13-3.263.50.19210680.9560.1190.2271.31199.3
3.26-3.413.60.1710680.9610.1050.2011.70399.3
3.41-3.583.60.14210700.9610.0880.1682.27698.7
3.58-3.813.60.12310680.9730.0760.1452.31998.8
3.81-4.13.50.10310910.9810.0640.1222.66699.4
4.1-4.523.50.08210750.9870.0510.0972.6598.5
4.52-5.173.50.07410610.990.0450.0872.5697.9
5.17-6.513.10.07210690.9880.0460.0862.76796.5
6.51-503.60.0711250.9910.0420.0824.41199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.27 Å45.55 Å
Translation4.27 Å45.55 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R3A

2r3a


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.164 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 856 4 %RANDOM
Rwork0.2123 ---
obs0.2147 20360 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.67 Å2 / Biso mean: 42.46 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0 Å21.04 Å2
2---3.71 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 60 44 3777
Biso mean--45.69 34.01 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193839
X-RAY DIFFRACTIONr_bond_other_d0.0020.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.081.945211
X-RAY DIFFRACTIONr_angle_other_deg0.8233.0067555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94924170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48915552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0741521
X-RAY DIFFRACTIONr_chiral_restr0.0590.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
LS refinement shellResolution: 2.404→2.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 64 -
Rwork0.277 1411 -
all-1475 -
obs--93.3 %

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