[English] 日本語
Yorodumi
- PDB-3f9y: Structural Insights into Lysine Multiple Methylation by SET Domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f9y
TitleStructural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy
Components
  • Histone H4
  • Histone-lysine N-methyltransferase SETD8
KeywordsTRANSFERASE / methyltransferase / histone / SET / lysine / Cell cycle / Cell division / Chromatin regulator / Chromosomal protein / Mitosis / Nucleus / Repressor / S-adenosyl-L-methionine / Transcription / Transcription regulation / DNA-binding / Methylation / Nucleosome core
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 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 / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / 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 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Beta Complex / 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: 1.5 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: Advisory / Version format compliance
Revision 1.2Apr 9, 2014Group: Refinement description
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 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 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,9126
Polymers40,1444
Non-polymers7692
Water4,089227
1
A: Histone-lysine N-methyltransferase SETD8
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4563
Polymers20,0722
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.5 kcal/mol
Surface area9240 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase SETD8
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4563
Polymers20,0722
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-8.1 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.400, 45.000, 52.400
Angle α, β, γ (deg.)91.40, 115.30, 89.80
Int Tables number1
Space group name H-MP1

-
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.: 2 / 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: 1297.576 Da / Num. of mol.: 2 / 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.64 %
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

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2006
RadiationMonochromator: Si(220) sagital focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 55907 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rsym value: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 1.5→1.6 Å / Mean I/σ(I) obs: 8.4 / Rsym value: 0.528

-
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: 1.5→23.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.931 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22012 2811 5 %RANDOM
Rwork0.19364 ---
obs0.19497 53407 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.05 Å20.1 Å2
2--0.21 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 52 227 2959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212801
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9943758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56923.431137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01715520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7171525
X-RAY DIFFRACTIONr_chiral_restr0.1230.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022091
X-RAY DIFFRACTIONr_nbd_refined0.2170.21246
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.224
X-RAY DIFFRACTIONr_mcbond_it1.2161.51721
X-RAY DIFFRACTIONr_mcangle_it1.86222652
X-RAY DIFFRACTIONr_scbond_it2.79431241
X-RAY DIFFRACTIONr_scangle_it4.0824.51106
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 203 -
Rwork0.334 3860 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.75620.52720.60242.3936-0.29684.10350.1429-0.1435-0.26960.16-0.0695-0.16780.33980.1593-0.0734-0.03320.0351-0.0135-0.15370.0267-0.1487-19.54-16.25418.124
23.0643-0.5651-0.63432.22810.55941.8998-0.03440.020.11250.1019-0.01030.1314-0.07220.01360.0447-0.02960.0012-0.0104-0.15520.0125-0.1686-1.698-0.414-0.111
31.35040.5185-0.8040.255-0.3120.8537-0.0267-0.0369-0.02450.01260.00090.00640.01790.04310.02580.09560.0279-0.0176-0.05240.0028-0.034-9.552-7.63178.5359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A194 - 352
2X-RAY DIFFRACTION1E16 - 22
3X-RAY DIFFRACTION2B193 - 352
4X-RAY DIFFRACTION2F16 - 23
5X-RAY DIFFRACTION3B1 - 186
6X-RAY DIFFRACTION3B353 - 393

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more