[English] 日本語
Yorodumi
- PDB-7p6y: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p6y
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / 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 / Bromodomain, conserved site ...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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-5Z1 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å
AuthorsChung, C.
CitationJournal: Chemistry / Year: 2021
Title: One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics.
Authors: Fallon, D.J. / Lehmann, S. / Chung, C.W. / Phillipou, A. / Eberl, C. / Fantom, K.G.M. / Zappacosta, F. / Patel, V.K. / Bantscheff, M. / Schofield, C.J. / Tomkinson, N.C.O. / Bush, J.T.
History
DepositionJul 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Bromodomain-containing protein 4
BBB: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9774
Polymers30,1992
Non-polymers1,7782
Water3,747208
1
AAA: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,0991
Non-polymers8891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,0991
Non-polymers8891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.035, 52.166, 59.957
Angle α, β, γ (deg.)90.000, 90.144, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-5Z1 / 4-benzoyl-N-(2-(2-(2-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)(methyl)amino)ethoxy)ethoxy)ethyl)-N-(2-oxo-2-((2-(2-(prop-2-yn-1-yloxy)ethoxy)ethyl)amino)ethyl)benzamide


Mass: 889.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H60N6O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 sodium citrate pH 5.6, 10% w/v PEG4K, 10% w/v propan-2-ol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.696
pseudo-merohedral22-h,-k,l20.304
ReflectionResolution: 1.88→59.96 Å / Num. obs: 20355 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1034 / CC1/2: 0.839 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 1.881→59.957 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.996 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.222 1071 5.262 %
Rwork0.177 19283 -
all0.179 --
obs-20354 95.775 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.513 Å2
Baniso -1Baniso -2Baniso -3
1--15.037 Å2-0 Å2-4.747 Å2
2--7.438 Å20 Å2
3---7.599 Å2
Refinement stepCycle: LAST / Resolution: 1.881→59.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 130 208 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132305
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172180
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.6613135
X-RAY DIFFRACTIONr_angle_other_deg1.1331.6615039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81825112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27715385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.478156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined0.1930.2508
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21975
X-RAY DIFFRACTIONr_nbtor_refined0.170.21083
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2137
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.223
X-RAY DIFFRACTIONr_nbd_other0.1850.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.212
X-RAY DIFFRACTIONr_mcbond_it2.6754.3721011
X-RAY DIFFRACTIONr_mcbond_other2.6594.371010
X-RAY DIFFRACTIONr_mcangle_it3.7719.8211262
X-RAY DIFFRACTIONr_mcangle_other3.779.8271263
X-RAY DIFFRACTIONr_scbond_it3.1335.11294
X-RAY DIFFRACTIONr_scbond_other3.1325.11295
X-RAY DIFFRACTIONr_scangle_it4.79811.1471873
X-RAY DIFFRACTIONr_scangle_other4.79711.1461874
X-RAY DIFFRACTIONr_lrange_it7.27440.7622754
X-RAY DIFFRACTIONr_lrange_other7.27340.7652755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.881-1.930.272880.2141313X-RAY DIFFRACTION89.578
1.93-1.9820.2491120.211352X-RAY DIFFRACTION96.5699
1.982-2.040.274780.2021352X-RAY DIFFRACTION96.8179
2.04-2.1030.21570.1981357X-RAY DIFFRACTION97.249
2.103-2.1710.264940.2341218X-RAY DIFFRACTION97.3294
2.171-2.2480.273530.2071208X-RAY DIFFRACTION92.381
2.248-2.3320.292510.2011101X-RAY DIFFRACTION88.1408
2.332-2.4270.307690.2091138X-RAY DIFFRACTION97.2603
2.427-2.5350.249530.2281132X-RAY DIFFRACTION98.4219
2.535-2.6590.269540.2011088X-RAY DIFFRACTION97.6068
2.659-2.8020.157601008X-RAY DIFFRACTION96.7391
2.802-2.9720.258400.19960X-RAY DIFFRACTION97.2763
2.972-3.1760.272410.185920X-RAY DIFFRACTION97.3658
3.176-3.430.231700.173818X-RAY DIFFRACTION97.6898
3.43-3.7560.14540780X-RAY DIFFRACTION96.3572
3.756-4.1970.184320.126701X-RAY DIFFRACTION97.344
4.197-4.8430.157390.119618X-RAY DIFFRACTION97.1893
4.843-5.9220.208200.163540X-RAY DIFFRACTION97.3913
5.922-8.3340.24680.175440X-RAY DIFFRACTION97.6035
8-100.238120.165239X-RAY DIFFRACTION95.0758

+
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://pdbjlvh1.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