Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / sperm DNA condensation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / male meiotic nuclear division / Estrogen-dependent gene expression / male meiosis I / regulation of RNA splicing / localization / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / spermatogenesis / chromatin remodeling / protein heterodimerization activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 7 Details: 15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.
Type: MARRESEARCH / Detector: CCD / Date: Nov 1, 2007
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.8726 Å / Relative weight: 1
Reflection
Resolution: 2.37→44 Å / Num. obs: 12142 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.1
Reflection shell
Resolution: 2.37→2.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 63.3
-
Processing
Software
Name
Version
Classification
CNS
1
refinement
XDS
datareduction
XSCALE
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: BROMODOMAIN BD2 FROM BRDT Resolution: 2.37→44 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE FOLLOWING RESIDUES WERE NOT MODELLED BECAUSE OF POOR DENSITY - CHAIN A RESIDUES 21-26, CHAIN B RESIDUES 18-26, CHAIN P RESIDUES 1-3 AND 13-20, CHAIN Q RESIDUES 1 AND 13-20. THE FOLLOWING ...Details: THE FOLLOWING RESIDUES WERE NOT MODELLED BECAUSE OF POOR DENSITY - CHAIN A RESIDUES 21-26, CHAIN B RESIDUES 18-26, CHAIN P RESIDUES 1-3 AND 13-20, CHAIN Q RESIDUES 1 AND 13-20. THE FOLLOWING RESIDUES WERE MODELLED AS ALANINE - CHAIN A RESIDUES 18-21, CHAIN P RESIDUE 12, AND CHAIN Q RESIDUE 12. FOLLOWING RESIDUES WERE MODELLED AS ALA: A18-21, P12, Q12.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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