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- PDB-3f9x: Structural Insights into Lysine Multiple Methylation by SET Domai... -

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Basic information

Entry
Database: PDB / ID: 3f9x
TitleStructural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy
Components
  • Histone H4
  • Histone-lysine N-methyltransferase SETD8
KeywordsTRANSFERASE / methyltransferase / histone / SET / lysine / Alternative splicing / Cell cycle / Cell division / Chromatin regulator / Chromosomal protein / Coiled coil / Mitosis / Nucleus / Repressor / S-adenosyl-L-methionine / Transcription / Transcription regulation / Acetylation / DNA-binding / Methylation / Nucleosome core
Function / homology
Function and homology information


lysine N-methyltransferase activity / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / mitotic chromosome condensation / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator ...lysine N-methyltransferase activity / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / mitotic chromosome condensation / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of double-strand break repair via homologous recombination / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / regulation of signal transduction by p53 class mediator / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. ...Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / 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 / Beta Complex / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCouture, J.-F. / Dirk, L.M.A. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural origins for the product specificity of SET domain protein methyltransferases.
Authors: Couture, J.F. / Dirk, L.M. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD8
B: Histone-lysine N-methyltransferase SETD8
C: Histone-lysine N-methyltransferase SETD8
D: Histone-lysine N-methyltransferase SETD8
E: Histone H4
F: Histone H4
G: Histone H4
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,88112
Polymers80,3438
Non-polymers1,5384
Water15,565864
1
A: Histone-lysine N-methyltransferase SETD8
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4703
Polymers20,0862
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7.8 kcal/mol
Surface area9440 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase SETD8
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4703
Polymers20,0862
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7.4 kcal/mol
Surface area9720 Å2
MethodPISA
3
C: Histone-lysine N-methyltransferase SETD8
G: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4703
Polymers20,0862
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-8.6 kcal/mol
Surface area9750 Å2
MethodPISA
4
D: Histone-lysine N-methyltransferase SETD8
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4703
Polymers20,0862
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8.7 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.112, 45.742, 94.760
Angle α, β, γ (deg.)89.45, 87.59, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Histone-lysine N-methyltransferase SETD8 / H4-K20-HMTase SETD8 / SET domain-containing protein 8 / PR/SET domain-containing protein 07 / ...H4-K20-HMTase SETD8 / SET domain-containing protein 8 / PR/SET domain-containing protein 07 / PR/SET07 / PR-Set7 / Lysine N-methyltransferase 5A


Mass: 18774.258 Da / Num. of mol.: 4 / Fragment: SET domain: UNP residues 232-393 / Mutation: Y334F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9NQR1, histone-lysine N-methyltransferase
#2: Protein/peptide
Histone H4


Mass: 1311.603 Da / Num. of mol.: 4 / Fragment: UNP residues 16-25 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to residues 16-25 of human histone H4
References: UniProt: P62805
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 204489 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.028 / Net I/σ(I): 30.4
Reflection shellResolution: 1.25→1.29 Å / Mean I/σ(I) obs: 9.9 / Rsym value: 0.131

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZKK

1zkk


Resolution: 1.25→47.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.592 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.053 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 9694 5 %RANDOM
Rwork0.18104 ---
obs0.18238 183160 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20.05 Å2
2--0.01 Å2-0.06 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.25→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5441 0 104 864 6409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215641
X-RAY DIFFRACTIONr_bond_other_d0.0020.023991
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9937569
X-RAY DIFFRACTIONr_angle_other_deg0.88139671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06323.285274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.835151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2321552
X-RAY DIFFRACTIONr_chiral_restr0.0970.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
X-RAY DIFFRACTIONr_nbd_refined0.2280.21031
X-RAY DIFFRACTIONr_nbd_other0.2160.24246
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22678
X-RAY DIFFRACTIONr_nbtor_other0.0850.22991
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2563
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.298
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0721.54379
X-RAY DIFFRACTIONr_mcbond_other1.4511.51386
X-RAY DIFFRACTIONr_mcangle_it2.47825357
X-RAY DIFFRACTIONr_scbond_it3.69132670
X-RAY DIFFRACTIONr_scangle_it4.7314.52212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 663 -
Rwork0.283 12197 -
obs--85.46 %

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