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- PDB-6jke: Discovery and the crystal structure of NS5 in complex with the N-... -

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Basic information

Entry
Database: PDB / ID: 6jke
TitleDiscovery and the crystal structure of NS5 in complex with the N-terminal bromodomain of BRD2.
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor
Function / homology
Function and homology information


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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BUX / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / TRIETHYLENE GLYCOL / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPadmanabhan, B. / Mathur, S. / Deshmukh, P.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)SR/WOS-A/LS-100/2013 India
Department of Biotechnology (DBT, India)ICMR No. 45/51/2018/PHA/BMS India
CitationJournal: Biochem.J. / Year: 2020
Title: Novel pyrano 1,3 oxazine based ligand inhibits the epigenetic reader hBRD2 in glioblastoma.
Authors: Deshmukh, P. / Mathur, S. / Gangadharan, G. / Krishnappa, G. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionFeb 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,48611
Polymers43,4163
Non-polymers1,0708
Water8,377465
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8408
Polymers28,9442
Non-polymers8966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-25 kcal/mol
Surface area11490 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2926
Polymers28,9442
Non-polymers3484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area3110 Å2
ΔGint-30 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.368, 55.750, 67.850
Angle α, β, γ (deg.)90.000, 94.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 14471.866 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a / Details (production host): pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25440

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Non-polymers , 7 types, 473 molecules

#2: Chemical ChemComp-BUX / 7-chloranyl-2-[(3-chlorophenyl)amino]pyrano[3,4-e][1,3]oxazine-4,5-dione


Mass: 325.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H6Cl2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.8M Ammonium sulphate, 100mM MES pH 6.5, 5mM DTT, PEG 10%, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.5→67.67 Å / Num. obs: 66509 / % possible obs: 97.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.87 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3209 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UYF

4uyf


Resolution: 1.5→67.67 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.57
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3376 5.08 %Random
Rwork0.186 63032 --
obs0.188 66408 97.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.88 Å2 / Biso mean: 24.8 Å2 / Biso min: 9.57 Å2
Refinement stepCycle: final / Resolution: 1.5→67.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 63 479 3230
Biso mean--48.52 38.88 -
Num. residues----322
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.52140.27661240.2635257795
1.5214-1.54420.28861490.2629250093
1.5442-1.56830.28611400.2466256296
1.5683-1.5940.26851590.2429265899
1.594-1.62150.27261340.214262799
1.6215-1.6510.25431450.2147265398
1.651-1.68270.22531330.216262897
1.6827-1.71710.26251500.2122262098
1.7171-1.75440.2111420.2109259497
1.7544-1.79520.2511390.2141259096
1.7952-1.84010.28241230.2183249892
1.8401-1.88990.22381350.2026264199
1.8899-1.94550.24141370.2067267599
1.9455-2.00830.23821470.2037266499
2.0083-2.08010.23231560.1963263799
2.0801-2.16340.24371440.1934262198
2.1634-2.26180.22421280.1889263596
2.2618-2.38110.22741270.1898254094
2.3811-2.53030.23131460.18812718100
2.5303-2.72570.20491390.1907268199
2.7257-30.24841610.1877264698
3-3.4340.21851110.1799261295
3.434-4.32640.19791490.14772721100
4.3264-670.2131580.1735273498

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