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- PDB-1zkk: Crystal structure of hSET8 in ternary complex with H4 peptide (16... -

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Basic information

Entry
Database: PDB / ID: 1zkk
TitleCrystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
Components
  • Histone-lysine N-methyltransferase, H4 lysine-20 specific
  • Peptide corresponding to residues 15-24 of histone H4
KeywordsTRANSFERASE / pseudo-knot / histone H4 / beta-sheet
Function / homology
Function and homology information


histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator ...histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / negative regulation of double-strand break repair via homologous recombination / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / regulation of signal transduction by p53 class mediator / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / 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 / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / 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 superfamily / SET domain / SET domain profile. / SET domain ...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 superfamily / SET domain / SET domain profile. / SET domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / Beta Complex / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / MAD, MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCouture, J.-F. / Collazo, E. / Brunzelle, J.S. / Trievel, R.C.
CitationJournal: Genes Dev. / Year: 2005
Title: Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
Authors: Couture, J.-F. / Collazo, E. / Brunzelle, J.S. / Trievel, R.C.
History
DepositionMay 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H4 lysine-20 specific
B: Histone-lysine N-methyltransferase, H4 lysine-20 specific
C: Histone-lysine N-methyltransferase, H4 lysine-20 specific
D: Histone-lysine N-methyltransferase, H4 lysine-20 specific
E: Peptide corresponding to residues 15-24 of histone H4
F: Peptide corresponding to residues 15-24 of histone H4
G: Peptide corresponding to residues 15-24 of histone H4
H: Peptide corresponding to residues 15-24 of histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,18512
Polymers80,6488
Non-polymers1,5384
Water18,1411007
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.960, 45.775, 94.435
Angle α, β, γ (deg.)89.22, 87.07, 90.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Histone-lysine N-methyltransferase, H4 lysine-20 specific / Histone H4-K20 methyltransferase / H4-K20-HMTase / SET domain-containing protein 8 / PR/SET domain- ...Histone H4-K20 methyltransferase / H4-K20-HMTase / SET domain-containing protein 8 / PR/SET domain-containing protein 07 / PR/SET07 / PR-Set7 / SET8


Mass: 18877.334 Da / Num. of mol.: 4 / Fragment: sequence database residues 231-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SET8, PRSET7, SET07 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21-DE3pLysS
References: UniProt: Q9NQR1, histone-lysine N-methyltransferase
#2: Protein/peptide
Peptide corresponding to residues 15-24 of histone H4


Mass: 1284.557 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Chain E, F, G, H are synthetic peptide from New England Peptide corresponding to residue 15-24 of the histone H4
References: UniProt: P62805*PLUS
#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.: 1007 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pentaerythritol ethoxylate, ammonium sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9686, 0.9792, 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2004
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97921
30.97911
ReflectionResolution: 1.45→22 Å / Num. obs: 122425 / % possible obs: 32 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.45→1.5 Å / % possible all: 34

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.45→19.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.134 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.083 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19902 6198 5 %RANDOM
Rwork0.16924 ---
all0.206 122425 --
obs0.17073 117760 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.084 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.03 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5434 0 104 1007 6545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215632
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9857554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.57323.333276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.594151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.91552
X-RAY DIFFRACTIONr_chiral_restr0.0850.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024196
X-RAY DIFFRACTIONr_nbd_refined0.1910.22548
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2835
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.291
X-RAY DIFFRACTIONr_mcbond_it0.9861.53470
X-RAY DIFFRACTIONr_mcangle_it1.51825344
X-RAY DIFFRACTIONr_scbond_it2.16232478
X-RAY DIFFRACTIONr_scangle_it3.1744.52210
X-RAY DIFFRACTIONr_rigid_bond_restr1.22835948
X-RAY DIFFRACTIONr_sphericity_free4.01631008
X-RAY DIFFRACTIONr_sphericity_bonded2.5435536
LS refinement shellResolution: 1.451→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 444 -
Rwork0.206 8436 -
obs--100 %

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