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- PDB-3b7b: EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) -

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Basic information

Entry
Database: PDB / ID: 3b7b
TitleEuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1)
ComponentsEuchromatic histone-lysine N-methyltransferase 1
KeywordsTRANSFERASE / Ankyrin repeat / Alternative splicing / ANK repeat / Chromatin regulator / Methyltransferase / Nucleus / Phosphorylation / Polymorphism / S-adenosyl-L-methionine
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 / Ankyrin repeats (many copies) / Ankyrin repeat-containing 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 / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsCollins, R.E. / Horton, J.R. / Cheng, X.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules
Authors: Collins, R.E. / Northrop, J.P. / Horton, J.R. / Lee, D.Y. / Zhang, X. / Stallcup, M.R. / Cheng, X.
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Euchromatic histone-lysine N-methyltransferase 1
B: Euchromatic histone-lysine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,12010
Polymers52,3512
Non-polymers7698
Water50428
1
A: Euchromatic histone-lysine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5605
Polymers26,1761
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Euchromatic histone-lysine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5605
Polymers26,1761
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.790, 151.260, 167.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Euchromatic histone-lysine N-methyltransferase 1 / Histone-lysine N-methyltransferase / H3 lysine-9 specific 5 / Histone H3-K9 methyltransferase 5 / ...Histone-lysine N-methyltransferase / H3 lysine-9 specific 5 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Eu-HMTase1 / G9a- like protein 1 / GLP1


Mass: 26175.650 Da / Num. of mol.: 2 / Fragment: Ankyrin repeat domains 2-7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus
References: UniProt: Q9H9B1, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2007
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.99→28.75 Å / Num. all: 16000 / Num. obs: 15965 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.7
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.535 / Num. unique all: 1564 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Generated Model from Phyre server

Resolution: 2.99→28.75 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 753 -RANDOM
Rwork0.205 ---
all0.208 15822 --
obs0.208 15490 97.9 %-
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1-13.26 Å20 Å20 Å2
2---2.15 Å20 Å2
3----11.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-28.75 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.99→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 40 28 3533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.99→3.1 Å / Rfactor Rfree error: 0.049
RfactorNum. reflection% reflection
Rfree0.395 65 -
Rwork0.378 --
obs-1466 94.6 %

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