[English] 日本語
Yorodumi
- PDB-7rui: Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rui
TitleBromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION/INHIBITOR / Selective BRD4-BD1 inhibitor / TRANSCRIPTION-INHIBITOR complex
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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / 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-7QZ / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRatia, K.M. / Xiong, R. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)UL1RR029879 United States
CitationJournal: To Be Published
Title: Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844
Authors: Xiong, R. / Ratia, K.M. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R.
History
DepositionAug 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8432
Polymers15,1231
Non-polymers7201
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.158, 42.303, 90.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 15123.376 Da / Num. of mol.: 1 / Fragment: bromodomain 1 (UNP residues 44-168)
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-7QZ / N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(5-{[(2-fluorophenyl)carbamoyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-1H-indol-4-yl}-2,2,2-trifluoroethane-1-sulfonamide


Mass: 719.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H29F4N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 0.1 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→42.3 Å / Num. obs: 31930 / % possible obs: 97 % / Redundancy: 5.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.036 / Rrim(I) all: 0.089 / Net I/σ(I): 11.7 / Num. measured all: 188859 / Scaling rejects: 16
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.363 / Num. unique obs: 1219 / CC1/2: 0.832 / Rpim(I) all: 0.239 / Rrim(I) all: 0.438 / % possible all: 77.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXF

3mxf


Resolution: 1.35→38.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.865 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 1586 5 %RANDOM
Rwork0.1692 ---
obs0.1702 30290 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.65 Å2 / Biso mean: 17.917 Å2 / Biso min: 11.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2---0.74 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.35→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 51 119 1235
Biso mean--17.31 25.4 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131151
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181030
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.7091575
X-RAY DIFFRACTIONr_angle_other_deg1.4781.5972411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84825.17258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.01153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 88 -
Rwork0.23 1782 -
all-1870 -
obs--77.72 %

+
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