[English] 日本語
Yorodumi
- PDB-7ug5: Second bromodomain of BRD3 liganded with BMS-536924 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ug5
TitleSecond bromodomain of BRD3 liganded with BMS-536924
ComponentsBromodomain-containing protein 3
KeywordsTRANSCRIPTION / bromodomain / small molecule ligand / complex
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / lysine-acetylated histone binding / molecular condensate scaffold activity / chromatin organization / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / 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-N6I / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of CBP and EP300 interaction with kinase inhibitors
Authors: Schonbrunn, E. / Bikowitz, M.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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 3
B: Bromodomain-containing protein 3
C: Bromodomain-containing protein 3
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,31022
Polymers52,3574
Non-polymers1,95318
Water10,377576
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6934
Polymers13,0891
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9418
Polymers13,0891
Non-polymers8527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3375
Polymers13,0891
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3375
Polymers13,0891
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.590, 92.280, 64.910
Angle α, β, γ (deg.)90.000, 99.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-717-

HOH

-
Components

#1: Protein
Bromodomain-containing protein 3 / RING3-like protein


Mass: 13089.126 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Chemical ChemComp-N6I / (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one


Mass: 479.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C25H26ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.8→19.8 Å / Num. obs: 56001 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.9 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.121 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4129 / CC1/2: 0.677 / Rrim(I) all: 0.887 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9L

7l9l


Resolution: 1.8→19.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1121 2 %
Rwork0.1878 54879 -
obs0.1886 56000 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.22 Å2 / Biso mean: 26.0203 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 132 578 4326
Biso mean--39.07 33.59 -
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.880.38571400.31976818695899
1.88-1.980.25861390.256268366975100
1.98-2.10.25441400.219368316971100
2.1-2.270.23181390.198368316970100
2.27-2.490.24521400.188968827022100
2.49-2.850.22671400.179868286968100
2.86-3.590.21181410.16968977038100
3.59-19.80.18561420.164669567098100

+
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