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- PDB-7l72: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -

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Basic information

Entry
Database: PDB / ID: 7l72
TitleCrystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280
ComponentsBromodomain-containing protein 3
KeywordsGENE REGULATION / BET / PLK1 / epigenetics
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-79C / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKarim, M.R. / Bikowitz, M. / 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
DepositionDec 25, 2020Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8512
Polymers13,3071
Non-polymers5441
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.580, 63.270, 40.040
Angle α, β, γ (deg.)90.000, 109.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13307.399 Da / Num. of mol.: 1
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-79C / 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 543.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35F2N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.5→37.63 Å / Num. obs: 19458 / % possible obs: 93 % / Redundancy: 2.057 % / Biso Wilson estimate: 8.33 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.073 / Χ2: 0.986 / Net I/σ(I): 12.83
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
1.5-1.541.270.0428.261612154312690.9920.05982.2
1.54-1.581.3610.0448.941775147413040.9890.06288.5
1.58-1.631.4430.0519.611961147413590.9840.07292.2
1.63-1.681.5230.0510.312012141913210.9820.07193.1
1.68-1.731.5690.04910.482021137612880.9860.0793.6
1.73-1.791.6530.05211.012030131912280.9830.07493.1
1.79-1.861.7040.04911.562023129111870.9830.06991.9
1.86-1.941.7380.05112.011992124211460.9840.07292.3
1.94-2.021.7660.05412.261953119811060.980.07692.3
2.02-2.121.8260.0512.751897113710390.9840.06991.4
2.12-2.241.920.05213.241930108510050.9830.07192.6
2.24-2.372.10.05613.88201010189570.9830.07494
2.37-2.542.4490.06115.1522659569250.9840.07796.8
2.54-2.742.8980.0616.7425368898750.9870.07398.4
2.74-33.4680.06418.5228618478250.9880.07697.4
3-3.353.4910.06918.6725527407310.9830.08298.8
3.35-3.873.5210.05918.8522996626530.9920.06998.6
3.87-4.743.4930.05918.6719845745680.9910.0799
4.74-6.713.4910.0618.814944354280.9890.07198.4
6.71-37.633.3290.06118.268092532430.9890.07396

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S92

3s92


Resolution: 1.5→37.63 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1817 973 5 %
Rwork0.1518 18485 -
obs0.1533 19458 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.67 Å2 / Biso mean: 12.3693 Å2 / Biso min: 3.45 Å2
Refinement stepCycle: final / Resolution: 1.5→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 39 204 1174
Biso mean--16.12 21.88 -
Num. residues----113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.580.17731250.1492380250585
1.58-1.680.1931380.14732633277193
1.68-1.810.22121390.15842639277894
1.81-1.990.18511380.15412622276092
1.99-2.280.18551370.15542594273192
2.28-2.870.20221450.15552762290797
2.87-37.630.15521510.14682855300699
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)
1-0.00010.01060.01150.09280.08620.08110.03490.0026-0.0039-0.0283-0.14120.00170.0594-0.0265-0.00550.06770.00820.0030.06290.00910.0729-12.8436-16.2624-7.7027
20.0296-0.0272-0.04470.05580.04340.05620.0204-0.13580.01870.0216-0.0298-0.0584-0.01510.1561-0.00020.0618-0.01560.00080.0965-0.00920.0584-17.1009-7.097914.0585
30.07920.0525-0.03670.0747-0.04590.02560.0023-0.0598-0.0054-0.0246-0.0217-0.05780.06370.0177-00.05580.0059-0.00170.04540.00920.0538-18.5616-15.6544.614
40.0704-0.03990.01540.0348-0.03220.03780.03190.02440.0848-0.0059-0.03590.02880.0277-0.0275-0.00130.0562-0.00760.00020.0413-0.00450.0633-23.2388-3.73711.4622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 323 )A304 - 323
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 357 )A324 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 390 )A358 - 390
4X-RAY DIFFRACTION4chain 'A' and (resid 391 through 416 )A391 - 416

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