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- PDB-2r3a: Methyltransferase domain of human suppressor of variegation 3-9 h... -

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Basic information

Entry
Database: PDB / ID: 2r3a
TitleMethyltransferase domain of human suppressor of variegation 3-9 homolog 2
ComponentsHistone-lysine N-methyltransferase SUV39H2
KeywordsTRANSFERASE / Histone H3-K9 methyltransferase 2 / Histone-lysine N-methyltransferase / H3 lysine-9 specific 2 / Alternative splicing / Cell cycle / Chromatin regulator / Chromosomal protein / Differentiation / Nucleus / Repressor / S-adenosyl-L-methionine / Telomere / Transcription / Transcription regulation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / S-adenosyl-L-methionine binding / epigenetic programming in the zygotic pronuclei / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / chromosome, centromeric region / ubiquitin-like ligase-substrate adaptor activity / circadian rhythm ...[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / S-adenosyl-L-methionine binding / epigenetic programming in the zygotic pronuclei / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / chromosome, centromeric region / ubiquitin-like ligase-substrate adaptor activity / circadian rhythm / PKMTs methylate histone lysines / chromatin organization / methylation / cellular response to hypoxia / cell differentiation / transcription cis-regulatory region binding / chromatin remodeling / 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 motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Beta-clip-like ...Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone H3-K9 methyltransferase / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Beta-clip-like / SET domain / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / 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 / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / SERINE / Histone-lysine N-methyltransferase SUV39H2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLunin, V.V. / Wu, H. / Zeng, H. / Ren, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Lunin, V.V. / Wu, H. / Zeng, H. / Ren, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Structural biology of human H3K9 methyltransferases
Authors: Wu, H. / Min, J. / Lunin, V.V. / Antoshenko, T. / Dombrovski, L. / Zeng, H. / Allali-Hassani, A. / Campagna-Slater, V. / Vedadi, M. / Arrowsmith, C.H. / Plotnikov, A.N. / Schapira, M.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7467
Polymers33,9811
Non-polymers7656
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.748, 63.925, 64.529
Angle α, β, γ (deg.)90.00, 109.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33980.547 Da / Num. of mol.: 1 / Fragment: Methyltransferase domain: Residues 112-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUV39H2 / Plasmid: p15MHL / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: Q9H5I1, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 10000, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 22956 / Num. obs: 22956 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.084 / Net I/σ(I): 15
Reflection shellResolution: 2→2.08 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2190 / Rsym value: 0.336 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MHV

1mhv
PDB Unreleased entry


Resolution: 2→35.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.647 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21252 1182 5.2 %RANDOM
Rwork0.17659 ---
all0.17851 21763 --
obs0.17851 21763 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.41 Å2
2---1.75 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 38 254 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9653024
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52323.945109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01715372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.61516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21009
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21537
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9661.51400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58522193
X-RAY DIFFRACTIONr_scbond_it2.5913965
X-RAY DIFFRACTIONr_scangle_it3.8334.5830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 80 -
Rwork0.224 1478 -
obs--89.18 %

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