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- PDB-6ddj: Crystal Structure of the human BRD2 BD2 bromodimain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ddj
TitleCrystal Structure of the human BRD2 BD2 bromodimain in complex with a Tetrahydroquinoline analogue
ComponentsBromodomain-containing protein 2
KeywordsTranscription/Inhibitor / BET / BRD2 / bromodomain / Inhibitor / Complex / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-G7V / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: Cancer Res. / Year: 2020
Title: Bromodomain-Selective BET Inhibitors Are Potent Antitumor Agents against MYC-Driven Pediatric Cancer.
Authors: Slavish, P.J. / Chi, L. / Yun, M.K. / Tsurkan, L. / Martinez, N.E. / Jonchere, B. / Chai, S.C. / Connelly, M. / Waddell, M.B. / Das, S. / Neale, G. / Li, Z. / Shadrick, W.R. / Olsen, R.R. / ...Authors: Slavish, P.J. / Chi, L. / Yun, M.K. / Tsurkan, L. / Martinez, N.E. / Jonchere, B. / Chai, S.C. / Connelly, M. / Waddell, M.B. / Das, S. / Neale, G. / Li, Z. / Shadrick, W.R. / Olsen, R.R. / Freeman, K.W. / Low, J.A. / Price, J.E. / Young, B.M. / Bharatham, N. / Boyd, V.A. / Yang, J. / Lee, R.E. / Morfouace, M. / Roussel, M.F. / Chen, T. / Savic, D. / Guy, R.K. / White, S.W. / Shelat, A.A. / Potter, P.M.
History
DepositionMay 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2067
Polymers13,5241
Non-polymers6826
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint11 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.357, 72.328, 32.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 13524.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25440
#2: Chemical ChemComp-G7V / 4-{[(2S,4R)-1-acetyl-2-methyl-6-(1H-pyrazol-3-yl)-1,2,3,4-tetrahydroquinolin-4-yl]amino}benzonitrile


Mass: 371.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEHPES, PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.049→50 Å / Num. obs: 56564 / % possible obs: 98.2 % / Redundancy: 13 % / Biso Wilson estimate: 9.32 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 1.228 / Net I/σ(I): 38.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.05-1.077.50.57333410.8360.210.6120.62993.7
1.07-1.110.10.49834120.8920.1590.5240.75596.2
1.1-1.1311.50.42234010.9290.1260.4410.87497.1
1.13-1.1612.40.36634840.9540.1060.3810.98397.2
1.16-1.1912.90.31334660.9670.0890.3261.03797.7
1.19-1.2313.40.28634890.9710.080.2971.08697.8
1.23-1.2713.70.25934950.9780.0720.2691.12698.2
1.27-1.3213.90.21935080.9850.060.2271.17698.6
1.32-1.38140.18435290.9880.0510.1911.23698.8
1.38-1.4614.10.15435560.9920.0420.161.27999.1
1.46-1.5514.10.1335490.9940.0360.1351.43599.3
1.55-1.6714.20.10835880.9960.030.1131.54199.6
1.67-1.8314.20.08935910.9970.0240.0931.51699.8
1.83-2.114.20.07136480.9980.020.0741.519100
2.1-2.6514.20.05736890.9980.0160.0591.402100
2.65-5012.80.0538180.9980.0150.0521.40798.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IG6

5ig6


Resolution: 1.05→32.004 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 10.19
RfactorNum. reflection% reflection
Rfree0.1292 2000 3.54 %
Rwork0.1155 --
obs0.116 56521 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.55 Å2 / Biso mean: 15.4243 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.05→32.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 99 148 1191
Biso mean--22.21 28 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091037
X-RAY DIFFRACTIONf_angle_d1.0471395
X-RAY DIFFRACTIONf_chiral_restr0.079136
X-RAY DIFFRACTIONf_plane_restr0.009181
X-RAY DIFFRACTIONf_dihedral_angle_d12.291391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.07570.18081310.1677357791
1.0757-1.10480.16581380.1486377397
1.1048-1.13730.14581400.1276379897
1.1373-1.1740.11841390.1013379797
1.174-1.2160.09141420.0899386698
1.216-1.26470.12381400.0895384098
1.2647-1.32220.10431430.0937388999
1.3222-1.39190.12541430.0897390299
1.3919-1.47910.11011440.0883392099
1.4791-1.59330.10011450.0861394699
1.5933-1.75370.11171460.09543986100
1.7537-2.00740.13431470.10484005100
2.0074-2.5290.11921480.11784032100
2.529-32.0040.15261540.1459419099

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