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- PDB-2rfi: Crystal structure of catalytic domain of human euchromatic histon... -

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Basic information

Entry
Database: PDB / ID: 2rfi
TitleCrystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide
Components
  • Histone H3
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
KeywordsTRANSFERASE / EUCHROMATIC HISTONE METHYLTRANSFERASE 1 / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / ANK repeat / Chromatin regulator / Nucleus / Phosphorylation / Polymorphism / S-adenosyl-L-methionine / Acetylation / Chromosomal protein / DNA damage / DNA repair / DNA-binding / Methylation / Nucleosome core
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription corepressor binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / 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: 1.59 Å
AuthorsMin, J. / Wu, H. / 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 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
P: Histone H3
Q: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,28114
Polymers67,9894
Non-polymers1,29210
Water12,358686
1
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0258
Polymers33,9952
Non-polymers1,0306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
Q: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2566
Polymers33,9952
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.593, 85.627, 95.670
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, H3 lysine-9 specific 5 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine N-methyltransferase ...Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP1


Mass: 32830.219 Da / Num. of mol.: 2 / Fragment: Catalytic domain: Residues 951-1235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876 / Plasmid: pET28a-thrombin-lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus
References: UniProt: Q9H9B1, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3


Mass: 1164.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic dimethylated H3K9 peptide
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2006 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→42.8 Å / Num. all: 89676 / Num. obs: 89676 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IGQ

2igq


Resolution: 1.59→42.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.708 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22014 4475 5 %RANDOM
Rwork0.19265 ---
all0.19403 85102 --
obs0.19403 85102 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.59→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 60 686 5068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.966065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6625534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2822.511235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13215733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8611554
X-RAY DIFFRACTIONr_chiral_restr0.080.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023514
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22064
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2582
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.52772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27224345
X-RAY DIFFRACTIONr_scbond_it1.77331974
X-RAY DIFFRACTIONr_scangle_it2.744.51720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 228 -
Rwork0.342 4267 -
obs--66.58 %

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