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- PDB-5jj0: Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH -

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Basic information

Entry
Database: PDB / ID: 5jj0
TitleStructure of G9a SET-domain with Histone H3K9M peptide and excess SAH
Components
  • Histone H3K9M mutant peptide
  • Histone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / SET-domain / Histone methyl transferase / histone peptide
Function / homology
Function and homology information


regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / DNA methylation-dependent constitutive heterochromatin formation / cellular response to cocaine / organ growth / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA replication / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / Transcriptional Regulation by VENTX / spermatid development / long-term memory / Chromatin modifying enzymes / response to fungicide / telomere organization / cellular response to starvation / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / transcription corepressor binding / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / cellular response to xenobiotic stimulus / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / response to ethanol / Estrogen-dependent gene expression / nuclear speck / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeat / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Histone H3 signature 1. / Ankyrin repeat / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone H3.1 / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsJayaram, H. / Bellon, S.F. / Poy, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3.
Authors: Jayaram, H. / Hoelper, D. / Jain, S.U. / Cantone, N. / Lundgren, S.M. / Poy, F. / Allis, C.D. / Cummings, R. / Bellon, S. / Lewis, P.W.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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 EHMT2
F: Histone H3K9M mutant peptide
B: Histone-lysine N-methyltransferase EHMT2
G: Histone H3K9M mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92314
Polymers65,6024
Non-polymers1,32010
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-18 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.667, 78.311, 73.056
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase EHMT2 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 ...Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Lysine N-methyltransferase 1C / Protein G9a


Mass: 31661.904 Da / Num. of mol.: 2
Fragment: SET domain of Histone-lysine N-methyltransferase EHMT2 G9a, UNP residues 882-1155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3K9M mutant peptide


Mass: 1139.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 178 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.001 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.72→45.91 Å / Num. obs: 63270 / % possible obs: 98.73 % / Redundancy: 3.6 % / Net I/σ(I): 10.13
Reflection shellResolution: 1.72→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.2 / % possible all: 87.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O8J

2o8j


Resolution: 1.72→45.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.309 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 3380 5.1 %RANDOM
Rwork0.21822 ---
obs0.21997 63270 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.777 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å21.58 Å2
2--0.64 Å20 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.72→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 62 130 4680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194694
X-RAY DIFFRACTIONr_bond_other_d0.0020.024302
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9656336
X-RAY DIFFRACTIONr_angle_other_deg1.1553.0059876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20523.719242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85315805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5711543
X-RAY DIFFRACTIONr_chiral_restr0.1180.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5772.9012246
X-RAY DIFFRACTIONr_mcbond_other2.5762.92245
X-RAY DIFFRACTIONr_mcangle_it3.5484.3332801
X-RAY DIFFRACTIONr_mcangle_other3.5474.3342802
X-RAY DIFFRACTIONr_scbond_it3.4343.3082448
X-RAY DIFFRACTIONr_scbond_other3.4333.3082449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.284.8013535
X-RAY DIFFRACTIONr_long_range_B_refined6.78223.2535188
X-RAY DIFFRACTIONr_long_range_B_other6.75623.2065155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 246 -
Rwork0.285 4111 -
obs--87.49 %

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