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- PDB-1peg: Structural basis for the product specificity of histone lysine me... -

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Basic information

Entry
Database: PDB / ID: 1peg
TitleStructural basis for the product specificity of histone lysine methyltransferases
Components
  • Histone H3
  • histone H3 methyltransferase DIM-5
KeywordsTRANSFERASE / Ternary structure of DIM-5 / a SUV39-type histone-H3 Lys-9 methyltransferase / SET domain protein forms a knot-like substructure / pre-SET triangular Zn3Cys9 zinc cluster / post-SET zinc-binding site / a hybrid beta sheet formed by DIM-5 and H3 tail
Function / homology
Function and homology information


SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / histone H3K9 trimethyltransferase activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair ...SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / histone H3K9 trimethyltransferase activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Chromatin modifying enzymes / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 / 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 / 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 / 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 / gene expression / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / methylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3 / Histone H3.1 / Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsZhang, X. / Yang, Z. / Khan, S.I. / Horton, J.R. / Tamaru, H. / Selker, E.U. / Cheng, X.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis for the product specificity of histone lysine methyltransferases
Authors: Zhang, X. / Yang, Z. / Khan, S.I. / Horton, J.R. / Tamaru, H. / Selker, E.U. / Cheng, X.
History
DepositionMay 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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.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_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 H3 methyltransferase DIM-5
P: Histone H3
B: histone H3 methyltransferase DIM-5
Q: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,64714
Polymers71,3554
Non-polymers1,29210
Water0
1
A: histone H3 methyltransferase DIM-5
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3237
Polymers35,6772
Non-polymers6465
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: histone H3 methyltransferase DIM-5
Q: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3237
Polymers35,6772
Non-polymers6465
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-124 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.260, 94.170, 114.690
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 H3 methyltransferase DIM-5


Mass: 34111.551 Da / Num. of mol.: 2 / Fragment: residues 17-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Plasmid: pXC379 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) Codon plus RIL (Stratagene)
Keywords: wild-type DIM-5
References: UniProt: Q8X225, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3 /


Mass: 1565.797 Da / Num. of mol.: 2 / Fragment: residues 1-15 / Source method: obtained synthetically
Details: The histone H3 peptide (N-terminal residues 1-15) is synthesized.
References: UniProt: P02303, UniProt: P68431*PLUS
#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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 289 K / pH: 8.4
Details: PEG 2000 monomethyl ether, trimethylamine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 8.40
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 9.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
220 mMglycine1droppH9.8
3150 mM1dropNaCl
45 mMdithiothreitol1drop
55 %glycerol1drop
6600000 nMAdoHcy1drop
70.1 MTris1reservoirpH8.4-8.6
820-25 %PEG2000 MME1reservoir
90.2 Mtrimethylamine1reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→35 Å / Num. obs: 21803 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 23.3
Reflection shellResolution: 2.59→2.68 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.228 / % possible all: 67.6
Reflection
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 35 Å
Reflection shell
*PLUS
% possible obs: 67.6 % / Num. unique obs: 1578 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ML9

1ml9


Resolution: 2.59→30.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINS WERE IMPOSED ON THE TWO COMPLEXES DURING THE REFINEMENT, EXCEPT THE POST-SET REGION RESIDUES 53 TO 100. MOLECULE B IS VERY FLEXIBLE IN THIS REGION ...Details: THE NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINS WERE IMPOSED ON THE TWO COMPLEXES DURING THE REFINEMENT, EXCEPT THE POST-SET REGION RESIDUES 53 TO 100. MOLECULE B IS VERY FLEXIBLE IN THIS REGION (ONLY THE CA ATOMS ARE GIVEN FOR THE RESIDUES 53 TO 87), WHILE THE CORRESPONDING REGION IN MOLECULE A IS ORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 943 4.8 %RANDOM
Rwork0.22 ---
obs0.22 19510 81.6 %-
all-19510 --
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--2.33 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.45 Å
Luzzati d res low-30.9 Å
Luzzati sigma a0.86 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.59→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 60 0 3618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.59→2.74 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 94 4.9 %
Rwork0.3 1825 -
obs--49 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77
LS refinement shell
*PLUS
Lowest resolution: 2.68 Å / Rfactor Rwork: 0.3

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