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- PDB-7mra: Crystal structure of the first bromodomain (BD1) of human BRD4 bo... -

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Basic information

Entry
Database: PDB / ID: 7mra
TitleCrystal structure of the first bromodomain (BD1) of human BRD4 bound to NC-II-259
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / Bromosporine / BRD4 / BRD / BET
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-ZMJ / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsChan, A. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1U54HD093540 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.
Authors: Guan, X. / Cheryala, N. / Karim, R.M. / Chan, A. / Berndt, N. / Qi, J. / Georg, G.I. / Schonbrunn, E.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5043
Polymers15,0991
Non-polymers4042
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.910, 42.770, 78.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-ZMJ / N-[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)phenyl]ethanesulfonamide


Mass: 342.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→34.17 Å / Num. obs: 41072 / % possible obs: 90.8 % / Redundancy: 12.767 % / Biso Wilson estimate: 12.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.066 / Χ2: 1.025 / Net I/σ(I): 20.14 / Num. measured all: 524382 / Scaling rejects: 622
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
1.16-1.1910.2780.8733.0218449331517950.6440.9254.1
1.19-1.2210.8820.7433.8524168321722210.8070.78169
1.22-1.2612.580.5855.534745310327620.9360.6189
1.26-1.313.4490.4727.138800305828850.9650.49194.3
1.3-1.3413.4690.3738.8437672293727970.9770.38795.2
1.34-1.3913.3120.31410.3736394285827340.9860.32795.7
1.39-1.4413.0720.26112.0534576276626450.9910.27295.6
1.44-1.512.8060.19314.9831632265024700.9930.20193.2
1.5-1.5614.0580.15718.7734737256124710.9950.16396.5
1.56-1.6413.8930.12522.1333106246723830.9960.1396.6
1.64-1.7313.6150.10724.8130839232322650.9960.11297.5
1.73-1.8313.1750.08928.3528484221621620.9980.09297.6
1.83-1.9612.3140.07731.524912208420230.9970.0897.1
1.96-2.1212.4040.06535.8123010195718550.9980.06794.8
2.12-2.3212.9160.05939.1222810179017660.9990.06298.7
2.32-2.5912.6030.05640.4320555164716310.9980.05999
2.59-312.2160.05541.1417664145714460.9980.05899.2
3-3.6710.9970.05140.0813317124812110.9990.05397
3.67-5.1912.4020.04443.51120059979680.9980.04697.1
5.19-34.1711.180.0440.8165075895820.9990.04298.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.16→34.17 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1864 1199 2.92 %
Rwork0.1755 39864 -
obs0.1759 41063 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.14 Å2 / Biso mean: 21.0175 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.16→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 28 187 1267
Biso mean--13.44 31.78 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.16-1.210.2953830.30712764284758
1.21-1.260.24621230.24534084420784
1.26-1.330.23321370.22464558469595
1.33-1.410.23041390.20544594473395
1.41-1.520.20211370.19164578471595
1.52-1.670.19971420.18134695483797
1.67-1.920.18391430.1844768491198
1.92-2.410.18361430.174768491197
2.41-34.170.16711520.15565055520798
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)
15.7471-3.06324.35467.8687-3.0695.8052-0.45310.07370.42710.3712-0.0488-0.5506-0.70090.29830.44940.1601-0.0245-0.02170.13220.0130.1579-4.0612.184-13.963
24.23892.26930.68623.37250.17872.1039-0.0148-0.0801-0.10580.0447-0.0283-0.1930.06730.03050.04580.08160.0180.00150.08560.00870.0741-11.249-5.281-4.264
30.78350.4942-0.92862.8082-3.45326.88680.0102-0.03580.02990.1122-0.0198-0.0266-0.21070.0558-0.01760.0801-0.0082-0.01530.0836-0.00690.0933-13.6954.213-10.227
42.67890.0702-0.04447.0651-4.49566.9596-0.04610.04410.2640.02050.0332-0.008-0.377-0.00260.04630.1033-0.005-0.03320.074-0.0130.1284-9.51612.477-3.781
50.338-1.49370.8737.0426-4.47663.49190.04250.05260.0220.0986-0.01570.077-0.09260.02050.00810.1204-0.0055-0.01680.1144-0.010.1027-14.354-2.182-20.67
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:75 )A61 - 75
2X-RAY DIFFRACTION2( CHAIN A AND RESID 76:106 )A76 - 106
3X-RAY DIFFRACTION3( CHAIN A AND RESID 107:144 )A107 - 144
4X-RAY DIFFRACTION4( CHAIN A AND RESID 145:167 )A145 - 167
5X-RAY DIFFRACTION5( CHAIN A AND RESID 42:60 )A42 - 60

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