[English] 日本語
Yorodumi
- PDB-5hq2: Structural model of Set8 histone H4 Lys20 methyltransferase bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hq2
TitleStructural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle
Components
  • (DNA (149-MER)) x 2
  • Guanine nucleotide exchange factor SRM1
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • N-lysine methyltransferase SETD8
KeywordsTransferase/DNA / chromatin enzyme / chromatin complex / epigenetics / histone methyltransferase / Transferase-DNA complex
Function / homology
Function and homology information


response to pheromone / 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 / Postmitotic nuclear pore complex (NPC) reformation / mitotic chromosome condensation ...response to pheromone / 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 / Postmitotic nuclear pore complex (NPC) reformation / mitotic chromosome condensation / protein-lysine N-methyltransferase activity / regulation of mitotic spindle assembly / regulation of DNA damage response, signal transduction by p53 class mediator / poly(A)+ mRNA export from nucleus / histone methyltransferase activity / nucleus organization / negative regulation of double-strand break repair via homologous recombination / ribosomal subunit export from nucleus / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Condensation of Prophase Chromosomes / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / protein import into nucleus / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nucleosome assembly / 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 / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. ...Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation (RCC1) repeat / Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Guanine nucleotide exchange factor SRM1 / Histone H4 / Histone H3.2 / Histone H2A / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsTavarekere, G. / McGinty, R.K. / Tan, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088236 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111651 United States
Damon Runyon Cancer Research FoundationDRG 2107-12 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.
Authors: Girish, T.S. / McGinty, R.K. / Tan, S.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8


Theoretical massNumber of molelcules
Total (without water)222,1678
Polymers222,1678
Non-polymers00
Water00
1
A: Histone H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8

A: Histone H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8


Theoretical massNumber of molelcules
Total (without water)444,33316
Polymers444,33316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)100.729, 300.752, 182.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsGel filtration used to confirm assembly

-
Components

-
Protein , 6 types, 6 molecules ABGHKM

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281
#7: Protein Guanine nucleotide exchange factor SRM1 / Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of ...Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of chromosome condensation / Suppressor of receptor mutations 1 / mRNA transport protein 1


Mass: 53095.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21827
#8: Protein N-lysine methyltransferase SETD8 / H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / ...H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / PR/SET domain-containing protein 07 / PR/SET07 / SET domain-containing protein 8


Mass: 23016.270 Da / Num. of mol.: 1 / Mutation: H347F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (149-MER)


Mass: 45772.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#6: DNA chain DNA (149-MER)


Mass: 46212.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: 25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
PH range: 5.5-6

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.5→46.19 Å / Num. all: 16854 / Num. obs: 16854 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.9
Reflection shellResolution: 4.5→4.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→46 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.832 / SU B: 124.392 / SU ML: 1.58 / Cross valid method: THROUGHOUT / ESU R Free: 1.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3972 845 5 %RANDOM
Rwork0.33904 ---
obs0.34184 15908 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 171.987 Å2
Baniso -1Baniso -2Baniso -3
1-11.93 Å20 Å2-0 Å2
2---7.31 Å20 Å2
3----4.62 Å2
Refinement stepCycle: LAST / Resolution: 4.5→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 2971 0 0 7738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0168112
X-RAY DIFFRACTIONr_bond_other_d0.0040.024618
X-RAY DIFFRACTIONr_angle_refined_deg0.991.61611783
X-RAY DIFFRACTIONr_angle_other_deg1.359310286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028379
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.96721.7973827
X-RAY DIFFRACTIONr_mcbond_other9.95121.7963826
X-RAY DIFFRACTIONr_mcangle_it17.74332.6584768
X-RAY DIFFRACTIONr_mcangle_other17.74332.664769
X-RAY DIFFRACTIONr_scbond_it10.88622.7294285
X-RAY DIFFRACTIONr_scbond_other10.88522.7314286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.72734.0127015
X-RAY DIFFRACTIONr_long_range_B_refined27.0759255
X-RAY DIFFRACTIONr_long_range_B_other27.0769256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.5→4.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 55 -
Rwork0.36 1125 -
obs--96.48 %

+
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