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- PDB-3mo2: human G9a-like (GLP, also known as EHMT1) in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 3mo2
Titlehuman G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67
ComponentsHistone-lysine N-methyltransferase, H3 lysine-9 specific 5Histone methyltransferase
KeywordsTRANSFERASE / Epigenetics / Histone lysine methylation / enzymatic inhibition / lysine mimics
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / facultative heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / : ...[histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / facultative heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / : / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / 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 domain / Pre-SET motif / 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 domain / Pre-SET motif / 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 superfamily / SET domain / 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
Chem-E67 / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChang, Y. / Horton, J.R. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases.
Authors: Chang, Y. / Ganesh, T. / Horton, J.R. / Spannhoff, A. / Liu, J. / Sun, A. / Zhang, X. / Bedford, M.T. / Shinkai, Y. / Snyder, J.P. / Cheng, X.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
C: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
D: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,33526
Polymers131,3214
Non-polymers4,01422
Water7,152397
1
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6426
Polymers32,8301
Non-polymers8115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6426
Polymers32,8301
Non-polymers8115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0267
Polymers32,8301
Non-polymers1,1966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0267
Polymers32,8301
Non-polymers1,1966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28312
Polymers65,6602
Non-polymers1,62310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area24030 Å2
MethodPISA
6
C: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
D: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,05214
Polymers65,6602
Non-polymers2,39212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-12 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.7, 163.0, 69.3
Angle α, β, γ (deg.)90.00, 98.9, 90.00
Int Tables number4
Space group name H-MP1211
Details4 complexes per asymmetric unit

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Components

#1: Protein
Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 / Histone methyltransferase / 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 / Lysine N-methyltransferase 1D


Mass: 32830.219 Da / Num. of mol.: 4 / Fragment: C-terminal SET domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876, KMT1D / 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.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-E67 / 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine


Mass: 549.751 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H47N7O2
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 51.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→31.83 Å / Num. obs: 43245 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.8
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.6 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FPD

3fpd


Resolution: 2.49→31.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 451338.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2107 5 %RANDOM
Rwork0.192 ---
obs0.192 41772 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8381 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å210.25 Å2
2---5.43 Å20 Å2
3---8.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-35 Å
Luzzati sigma a0.33 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.49→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8094 0 228 397 8719
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.952.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.49→2.58 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.308 195 5.1 %
Rwork0.266 3640 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water.paramion.top
X-RAY DIFFRACTION4E67_mod.parE67_mod.top
X-RAY DIFFRACTION5sah_xplor.parsah_xplor.top

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