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- PDB-5cpr: The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics... -

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Basic information

Entry
Database: PDB / ID: 5cpr
TitleThe novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity
ComponentsHistone-lysine N-methyltransferase SUV420H1
KeywordsTRANSFERASE / protein lysine transferase / H4K20 / non-homologous end joining
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 / metal ion binding / nucleus
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
Chem-539 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase KMT5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsJakob, C.G. / Upadhyay, A.K. / Sun, C.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity.
Authors: Bromberg, K.D. / Mitchell, T.R. / Upadhyay, A.K. / Jakob, C.G. / Jhala, M.A. / Comess, K.M. / Lasko, L.M. / Li, C. / Tuzon, C.T. / Dai, Y. / Li, F. / Eram, M.S. / Nuber, A. / Soni, N.B. / ...Authors: Bromberg, K.D. / Mitchell, T.R. / Upadhyay, A.K. / Jakob, C.G. / Jhala, M.A. / Comess, K.M. / Lasko, L.M. / Li, C. / Tuzon, C.T. / Dai, Y. / Li, F. / Eram, M.S. / Nuber, A. / Soni, N.B. / Manaves, V. / Algire, M.A. / Sweis, R.F. / Torrent, M. / Schotta, G. / Sun, C. / Michaelides, M.R. / Shoemaker, A.R. / Arrowsmith, C.H. / Brown, P.J. / Santhakumar, V. / Martin, A. / Rice, J.C. / Chiang, G.G. / Vedadi, M. / Barsyte-Lovejoy, D. / Pappano, W.N.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,7484
Polymers30,9251
Non-polymers8233
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.209, 47.913, 129.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30924.996 Da / Num. of mol.: 1 / Fragment: Set Domain residues 69-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUV420H1, KMT5B, CGI-85 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4FZB7, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-539 / 6,7-dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine


Mass: 359.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16Cl2N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The purified protein was concentrated to 10 mg/mL and with 1 mM SAM. SAM bound protein crystals were obtained by hanging drop vapor diffusion method at 17C using 10% (w/v) ethanol, 5% (w/v) ...Details: The purified protein was concentrated to 10 mg/mL and with 1 mM SAM. SAM bound protein crystals were obtained by hanging drop vapor diffusion method at 17C using 10% (w/v) ethanol, 5% (w/v) glycerol, 0.1 M tris pH 8.5 as the well solution. A-196 was soaked into the crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.217→47.913 Å / Num. obs: 13537 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.7
Reflection shellResolution: 2.217→2.225 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S8P

3s8p


Resolution: 2.22→38.47 Å / Cor.coef. Fo:Fc: 0.9138 / Cor.coef. Fo:Fc free: 0.8876 / SU R Cruickshank DPI: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 660 4.93 %RANDOM
Rwork0.1901 ---
obs0.1929 13393 98.95 %-
Displacement parametersBiso mean: 37.52 Å2
Baniso -1Baniso -2Baniso -3
1-9.9431 Å20 Å20 Å2
2--6.9451 Å20 Å2
3----16.8881 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: 1 / Resolution: 2.22→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 52 144 2014
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011910HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.142576HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d662SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1910HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2256SEMIHARMONIC4
LS refinement shellResolution: 2.22→2.4 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.305 116 4.4 %
Rwork0.2019 2522 -
all0.2062 2638 -
obs--97.24 %

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