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- PDB-7mr9: Crystal structure of the first bromodomain (BD1) of human BRD4 bo... -

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Basic information

Entry
Database: PDB / ID: 7mr9
TitleCrystal structure of the first bromodomain (BD1) of human BRD4 bound to NC-II-153
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-ZMM / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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)15,6045
Polymers15,0991
Non-polymers5054
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.440, 44.310, 77.980
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 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-ZMM / 2-methyl-4-[3-(2-oxopyrrolidin-1-yl)phenyl]isoquinolin-1(2H)-one


Mass: 318.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 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: 1.19→38.52 Å / Num. obs: 38288 / % possible obs: 90.3 % / Redundancy: 13.424 % / Biso Wilson estimate: 8.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.1 / Χ2: 0.957 / Net I/σ(I): 18.31 / Num. measured all: 513971 / Scaling rejects: 700
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
1.19-1.2212.170.6336.7421747308417870.8890.66357.9
1.22-1.2512.8770.5287.931896300724770.9530.5582.4
1.25-1.2913.450.4589.1836637295627240.9740.47792.2
1.29-1.3314.0070.40210.5536713283926210.9830.41792.3
1.33-1.3713.8380.34211.5135701276925800.9880.35593.2
1.37-1.4213.620.27612.9233683267424730.9890.28792.5
1.42-1.4813.3290.23714.0430176257822640.9890.24687.8
1.48-1.5414.2750.20116.2333204248923260.9940.20893.5
1.54-1.614.2340.17218.1732481240122820.9940.17895
1.6-1.6814.0690.14919.7730587228021740.9940.15595.4
1.68-1.7713.7680.1321.3529271222221260.9940.13595.7
1.77-1.8813.2960.11223.0726379206419840.9940.11696.1
1.88-2.0112.9430.09825.5422611195617470.9960.10289.3
2.01-2.1713.5780.08628.4724006181917680.9970.0997.2
2.17-2.3813.5070.08230.122070168816340.9970.08596.8
2.38-2.6613.0480.0830.4119494153714940.9970.08397.2
2.66-3.0712.6560.0753116871137013330.9970.07897.3
3.07-3.7611.9840.07131.0812415118110360.9970.07487.7
3.76-5.3212.7370.06332.7116809309170.9980.06698.6
5.32-38.5211.7360.06331.2763495485410.9980.06698.7

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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: 1.19→38.52 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 1199 3.13 %
Rwork0.1726 37075 -
obs0.173 38274 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.19 Å2 / Biso mean: 12.8306 Å2 / Biso min: 5.91 Å2
Refinement stepCycle: final / Resolution: 1.19→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 36 201 1287
Biso mean--11.38 21.27 -
Num. residues----127
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 (%)
1.19-1.240.2326920.23062851294364
1.24-1.290.23221340.19154122425691
1.29-1.360.19371340.16894151428593
1.36-1.450.17481360.16044193432993
1.45-1.560.18091320.15714114424691
1.56-1.720.16851400.16134335447595
1.72-1.960.19821410.16844355449695
1.96-2.470.19471410.17354365450695
2.48-38.520.17011490.17494589473896
Refinement TLS params.Method: refined / Origin x: 12.0625 Å / Origin y: 3.1755 Å / Origin z: 8.2928 Å
111213212223313233
T0.0377 Å2-0.0022 Å2-0.0029 Å2-0.0578 Å20.0046 Å2--0.0553 Å2
L0.4453 °2-0.0967 °20.0852 °2-0.9187 °20.146 °2--1.164 °2
S-0.011 Å °-0.0141 Å °0.0086 Å °0.0184 Å °0.0016 Å °0.0049 Å °-0.0626 Å °-0.0176 Å °0.0117 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 168
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allS2 - 209

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