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- PDB-3b95: EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 2) -

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Basic information

Entry
Database: PDB / ID: 3b95
TitleEuHMT1 (Glp) Ankyrin Repeat Domain (Structure 2)
Components
  • Euchromatic histone-lysine N-methyltransferase 1
  • Histone H3 N-terminal Peptide
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / Ankyrin repeat / ANK repeat / Methyltransferase / Transferase / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / transcription corepressor binding / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / methyltransferase activity / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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 / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) ...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 / Ankyrin repeat-containing 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 / Ankyrin repeats (3 copies) / Histone H3 signature 1. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Histone H3 signature 2. / Ankyrin repeat / Histone H3 / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Histone H3.1 / : / 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
DepositionNov 2, 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 1, 2012Group: Derived calculations
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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-lysine N-methyltransferase 1
B: Euchromatic histone-lysine N-methyltransferase 1
P: Histone H3 N-terminal Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,90513
Polymers53,9443
Non-polymers96110
Water50428
1
A: Euchromatic histone-lysine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6566
Polymers26,1761
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Euchromatic histone-lysine N-methyltransferase 1
P: Histone H3 N-terminal Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2497
Polymers27,7682
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.520, 152.390, 167.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe asymmetric unit contains two molecules (chain ID A and B), of which one (chain ID B) contains H3 peptide (chain ID P).

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Components

#1: Protein Euchromatic histone-lysine N-methyltransferase 1


Mass: 26175.650 Da / Num. of mol.: 2 / Fragment: Ankyrin repeat domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: Q5VT56, UniProt: Q9H9B1*PLUS
#2: Protein/peptide Histone H3 N-terminal Peptide


Mass: 1592.843 Da / Num. of mol.: 1 / Fragment: H3 Amino Terminus Peptide / Source method: obtained synthetically / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / 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: 3.41 Å3/Da / Density % sol: 63.88 %
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 13, 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→24.91 Å / Num. all: 15898 / Num. obs: 15898 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1559 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
GLRFphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 3B7B

3b7b


Resolution: 2.99→24.91 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 742 -RANDOM
Rwork0.195 ---
all0.203 15898 --
obs0.198 15329 97.1 %-
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-5.54 Å20 Å20 Å2
2---2.1 Å20 Å2
3----3.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-24.91 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.99→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 50 28 3623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.99→3.1 Å / Rfactor Rfree error: 0.047
RfactorNum. reflection% reflection
Rfree0.385 67 -
Rwork0.346 --
obs-1381 93.1 %

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