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- PDB-1o9s: Crystal structure of a ternary complex of the human histone methy... -

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Basic information

Entry
Database: PDB / ID: 1o9s
TitleCrystal structure of a ternary complex of the human histone methyltransferase SET7/9
Components
  • GENE FRAGMENT FOR HISTONE H3
  • HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
KeywordsTRANSFERASE / METHYLATION / HISTONE H3 / METHYLTRANSFERASE
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / Chromatin modifying enzymes / telomere organization ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / p53 binding / nucleosome / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / response to ethanol / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / : / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / : / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Single Sheet / 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 H3.1 / : / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsXiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J.
CitationJournal: Nature / Year: 2003
Title: Structure and Catalytic Mechanism of the Human Histone Methyltransferase Set7/9
Authors: Xiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J.
History
DepositionDec 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
B: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
K: GENE FRAGMENT FOR HISTONE H3
L: GENE FRAGMENT FOR HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0726
Polymers60,3034
Non-polymers7692
Water11,890660
1
A: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
K: GENE FRAGMENT FOR HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5363
Polymers30,1522
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
L: GENE FRAGMENT FOR HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5363
Polymers30,1522
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.690, 75.438, 69.099
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE DIMER IN THIS ENTRY IS FORMED BY THE COMPLEXOF CHAIN A WITH A PEPTIDE CHAIN K AND CHAIN B WITHPEPTIDE CHAIN L. CHAINS A AND B ARE MONOMERIC IN THEPHYSIOLOGICAL STATE.

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Components

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC / HISTONE H3-K4 METHYLTRANSFERASE / H3-K4-HMTASE


Mass: 28912.133 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, SET-DOMAIN, RESIDUES 108-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide GENE FRAGMENT FOR HISTONE H3


Mass: 1239.447 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-11 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16776, UniProt: P68431*PLUS
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growpH: 7.8 / Details: pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 54703 / % possible obs: 89.9 % / Redundancy: 22 % / Rsym value: 0.055 / Net I/σ(I): 47.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3I

1h3i


Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2440 5 %RANDOM
Rwork0.205 ---
obs0.206 54441 89.9 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 50 660 4754

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