[English] 日本語
Yorodumi
- PDB-7l9g: Crystal structure of the second bromodomain (BD2) of human BRD2 b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l9g
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 bound to BI2536
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-R78 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKarim, M.R. / Bikowitz, M.J. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionJan 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0575
Polymers13,3751
Non-polymers6814
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.530, 71.550, 32.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-504-

CL

21A-783-

HOH

-
Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13375.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.36→35.775 Å / Num. obs: 24096 / % possible obs: 90 % / Redundancy: 3.48 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.025 / Χ2: 1.005 / Net I/σ(I): 32.15 / Num. measured all: 83854 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.36-1.41.9590.1484.712118196210810.9520.19355.1
1.4-1.432.4260.1157.263297190413590.970.14571.4
1.43-1.482.6550.0929.133876183014600.9860.11479.8
1.48-1.522.8430.0811.634315178815180.990.09884.9
1.52-1.572.9710.06414.624585173715430.9940.07888.8
1.57-1.633.0720.05517.594863171015830.9960.06692.6
1.63-1.693.1610.04720.664861162715380.9970.05794.5
1.69-1.763.2280.04223.334820155814930.9980.0595.8
1.76-1.833.2970.03627.034817151014610.9980.04296.8
1.83-1.923.3470.03132.24853146614500.9990.03798.9
1.92-2.033.3980.02638.064587136913500.9990.03198.6
2.03-2.153.4220.02541.84497132413140.9990.02999.2
2.15-2.33.4550.02346.184225123412230.9990.02799.1
2.3-2.483.5530.02148.764065115111440.9990.02599.4
2.48-2.723.7620.02152.43976105910570.9990.02499.8
2.72-3.044.2820.0259.5741499769690.9990.02399.3
3.04-3.515.9340.0272.16509786485910.02299.4
3.51-4.36.7070.01980.33499774774510.0299.7
4.3-6.086.4130.01877.738486016000.9990.0299.8
6.08-35.7755.7540.0273.1200835934910.02297.2

-
Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 1.36→35.77 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 1085 4.5 %
Rwork0.149 23008 -
obs0.1501 24093 89.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 17.2205 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.36→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 98 209 1217
Biso mean--25.16 29.11 -
Num. residues----110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009983
X-RAY DIFFRACTIONf_angle_d1.4991324
X-RAY DIFFRACTIONf_dihedral_angle_d14.155136
X-RAY DIFFRACTIONf_chiral_restr0.079131
X-RAY DIFFRACTIONf_plane_restr0.008167
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 (%)
1.36-1.420.2512910.23131926201761
1.42-1.50.20531170.16252494261180
1.5-1.590.18341330.14922804293789
1.59-1.710.17641400.15152984312494
1.71-1.890.18181450.14563083322897
1.89-2.160.14281490.14143146329599
2.16-2.720.17171510.13693209336099
2.72-35.770.17011590.15183362352199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8293-1.46111.90692.373-2.06223.7051-0.0749-0.020.10320.01690.0366-0.0535-0.20810.10580.06580.0846-0.04430.00670.0888-0.01380.07739.743611.38032.5035
21.228-1.4621-0.55154.6421-0.58650.85940.01070.0137-0.0363-0.1249-0.0267-0.15090.08350.17480.01750.06070.02520.00380.10920.00320.074518.5643-7.51130.4239
34.267-0.28822.12843.9313-2.55118.40430.04160.21490.063-0.2428-0.1051-0.121-0.13510.29870.04860.1115-0.00850.02290.0862-0.01690.069512.48098.2099-9.2926
41.239-0.5001-0.29872.0751-0.30351.617-0.0076-0.03760.0360.04050.0590.0431-0.0050.0375-0.05230.0371-0.0149-0.00040.049-0.00930.06895.34621.20573.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 346 through 372 )A346 - 372
2X-RAY DIFFRACTION2chain 'A' and (resid 373 through 395 )A373 - 395
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 410 )A396 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 455 )A411 - 455

+
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