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- PDB-5uoo: BRD4 bromodomain 2 in complex with CD161 -

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Basic information

Entry
Database: PDB / ID: 5uoo
TitleBRD4 bromodomain 2 in complex with CD161
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Bromodomain
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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 / chromatin / 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 / 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 protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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-8FV / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Discovery of 4-(6-Methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indol-7-yl)-3,5-dimethylisoxazole (CD161) as a Potent and Orally Bioavailable BET Bromodomain Inhibitor.
Authors: Zhao, Y. / Bai, L. / Liu, L. / McEachern, D. / Stuckey, J.A. / Meagher, J.L. / Yang, C.Y. / Ran, X. / Zhou, B. / Hu, Y. / Li, X. / Wen, B. / Zhao, T. / Li, S. / Sun, D. / Wang, S.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Data collection / Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,2671
Non-polymers4351
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.188, 72.793, 32.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

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Components

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


Mass: 15266.552 Da / Num. of mol.: 1 / Fragment: UNP residues 333-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-8FV / 7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indole


Mass: 435.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 60% peg 400, 0.1M Imidizole, 5mM ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.69→29.38 Å / Num. obs: 14010 / % possible obs: 97.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.32 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.094 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.7-1.735.50.4180.956187.1
1.73-1.766.70.3920.997198.7
1.76-1.796.60.3381.078198.1
1.79-1.836.70.291.018197.7
1.83-1.876.50.2721.133198.6
1.87-1.916.40.2281.237198.9
1.91-1.966.50.1941.24198.8
1.96-2.026.30.1671.321198.5
2.02-2.076.30.1421.216198
2.07-2.146.10.1261.318197.8
2.14-2.2260.1061.239198.2
2.22-2.3160.0921.124198
2.31-2.4160.0831.122197.9
2.41-2.545.80.0721.046197.5
2.54-2.75.80.0651.038198.8
2.7-2.915.90.0641.11198.7
2.91-3.25.80.0551.108198.5
3.2-3.6660.050.939199.3
3.66-4.616.10.0440.77198.8
4.61-5060.0460.863198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→29.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.196 707 5.06 %RANDOM
Rwork0.175 ---
obs0.176 13979 98 %-
Displacement parametersBiso max: 78.52 Å2 / Biso mean: 21.32 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.0373 Å20 Å20 Å2
2--2.4983 Å20 Å2
3----0.461 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.69→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 67 105 1084
Biso mean--24.08 35.57 -
Num. residues----113
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d460SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes207HARMONIC5
X-RAY DIFFRACTIONt_it1031HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1311SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1031HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1418HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion2.61
LS refinement shellResolution: 1.69→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.202 144 5.27 %
Rwork0.169 2587 -
all0.171 2731 -
obs--95.58 %
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)
12.2269-1.38541.01313.5776-1.6662.6742-0.00170.07720.0252-0.02940.01080.0392-0.08570.0672-0.009-0.0403-0.0263-0.0025-0.024-0.0129-0.03759.785511.08581.5308
21.0553-1.1075-0.35090.2387-0.611900.0141-0.1128-0.2750.0101-0.0368-0.2627-0.07270.24640.0227-0.03570.0102-0.00790.0366-0.00190.077521.6094-3.29922.1692
30.3177-1.176-0.02586.3279-0.737300.04650.0452-0.0239-0.279-0.069-0.38980.05670.10530.0224-0.03790.0155-0.0043-0.0149-0.0099-0.008716.7801-8.6649-0.8293
41.1211-1.0583-2.67771.05251.1182.4419-0.03740.0277-0.1197-0.1663-0.0267-0.0795-0.21060.00870.06410.0324-0.02940.00290.0549-0.0019-0.034714.96228.472-8.6245
51.0172-0.3021-0.06421.6045-0.28640.92190.07430.1169-0.13770.021-0.02440.145-0.07590.0465-0.05-0.0429-0.0014-0.0029-0.0187-0.0221-0.02817.2274-1.3072-2.243
60.00020.34070.54321.2321.27681.80320.0381-0.1977-0.0180.1293-0.0437-0.13040.26740.05810.0056-0.0071-0.0116-0.01520.0410.0205-0.020510.3699-4.732312.9273
72.4105-1.31681.37833.0171-2.21354.61010.05630.04620.17510.00010.08910.1547-0.1306-0.1277-0.1454-0.0294-0.00470.00460.00070.0034-0.00010.81568.59182.5614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|348 - 376}A348 - 376
2X-RAY DIFFRACTION2{A|377 - 383}A377 - 383
3X-RAY DIFFRACTION3{A|384 - 402}A384 - 402
4X-RAY DIFFRACTION4{A|403 - 410}A403 - 410
5X-RAY DIFFRACTION5{A|411 - 435}A411 - 435
6X-RAY DIFFRACTION6{A|436 - 443}A436 - 443
7X-RAY DIFFRACTION7{A|444 - 460}A444 - 460

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