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- PDB-2igq: Human euchromatic histone methyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 2igq
TitleHuman euchromatic histone methyltransferase 1
Componentseuchromatic histone methyltransferase 1
KeywordsTRANSFERASE / euchromatic histone methyltransferase 1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / facultative heterochromatin formation / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / facultative heterochromatin formation / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 / Transcriptional Regulation by VENTX / regulation of embryonic development / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / transcription corepressor binding / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / positive regulation of cold-induced thermogenesis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / nuclear body / 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 EHMT1 / 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 EHMT1 / 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 / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMin, J. / Wu, H. / Antoshenko, T. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / 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
DepositionSep 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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: euchromatic histone methyltransferase 1
B: euchromatic histone methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,95312
Polymers65,6602
Non-polymers1,29210
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-12 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.520, 95.863, 102.124
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 euchromatic histone methyltransferase 1 / ehmt1 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine / Histone- ...ehmt1 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine / Histone-lysine N-methyltransferase / H3 lysine-9 specific 5 N-methyltransferase 1 / Eu-HMTase1 / G9a- like protein 1 / GLP1


Mass: 32830.219 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 951-1235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9B1, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4K, 10% Isoproponol, 0.1M Hepes 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2006
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→69.84 Å / Num. all: 44160 / Num. obs: 44160 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4115 / Rsym value: 0.58 / % possible all: 83.2

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Processing

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

1mvh


Resolution: 2→42.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.446 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23714 2365 5.1 %RANDOM
Rwork0.18866 ---
all0.19121 44160 --
obs0.19121 44160 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.145 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---1.61 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 60 566 4708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214236
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9575735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74822.611226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68215681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0551550
X-RAY DIFFRACTIONr_chiral_restr0.1030.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023335
X-RAY DIFFRACTIONr_nbd_refined0.1930.21905
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2443
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.214
X-RAY DIFFRACTIONr_mcbond_it0.9521.52626
X-RAY DIFFRACTIONr_mcangle_it1.50624096
X-RAY DIFFRACTIONr_scbond_it2.2731882
X-RAY DIFFRACTIONr_scangle_it3.4894.51639
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 130 -
Rwork0.327 2760 -
obs--79.03 %

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