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- PDB-4lys: Crystal Structure of BRD4(1) bound to Colchiceine -

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Basic information

Entry
Database: PDB / ID: 4lys
TitleCrystal Structure of BRD4(1) bound to Colchiceine
ComponentsBromodomain-containing protein 4BRD4
KeywordsPROTEIN BINDING/INHIBITOR / bromodomain / BRD4 inhibitor / epigenetic reader protein / acetylated lysine / histone tail / nucleus / PROTEIN BINDING-INHIBITOR complex
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 / transcription coregulator activity ...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 / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / 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 / 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-2SJ / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsWohlwend, D. / Gerhardt, S. / Einsle, O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: 4-Acyl pyrroles: mimicking acetylated lysines in histone code reading.
Authors: Lucas, X. / Wohlwend, D. / Hugle, M. / Schmidtkunz, K. / Gerhardt, S. / Schule, R. / Jung, M. / Einsle, O. / Gunther, S.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Non-polymer description / Structure summary

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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)15,4444
Polymers15,0121
Non-polymers4313
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.047, 108.072, 30.464
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-201-

NA

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 15012.301 Da / Num. of mol.: 1 / Fragment: FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60885
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2SJ / N-[(7S)-10-hydroxy-1,2,3-trimethoxy-9-oxo-5,6,7,9-tetrahydrobenzo[a]heptalen-7-yl]acetamide / Colchiceine


Mass: 385.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23NO6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: bis tris, PEG 3350, NaCl, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: VariMax VHF focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.83→41.047 Å / Num. all: 12331 / Num. obs: 12331 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.089 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.83-1.932.50.4091.9436717290.40997.3
1.93-2.0530.3222.4500116930.32299.4
2.05-2.1930.2173.6477615790.21799.8
2.19-2.373.10.1724.5449014620.17298.3
2.37-2.593.10.1345.8422513610.13499.3
2.59-2.93.10.0978.1388612530.09799.7
2.9-3.353.10.0613.1349211290.0699.5
3.35-4.13.10.04118.828739400.04198.2
4.1-5.830.03421.922797530.03497.9
5.8-41.0472.80.02826.212184320.02894.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.457 / Cor.coef. Fo:Fc: 0.445 / Cor.coef. Io to Ic: 0.448
Highest resolutionLowest resolution
Rotation3.5 Å10 Å
Translation3.5 Å10 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→29.34 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2333 / WRfactor Rwork: 0.1825 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7961 / SU B: 9.507 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2307 / SU Rfree: 0.1973 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.267 464 4.9 %RANDOM
Rwork0.2159 ---
obs0.2185 9566 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.06 Å2 / Biso mean: 18.6806 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å2-0 Å2
2---0.24 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 30 121 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021097
X-RAY DIFFRACTIONr_bond_other_d0.0030.0223
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9991495
X-RAY DIFFRACTIONr_angle_other_deg1.974348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6965123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11325.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12515192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.835153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022851
X-RAY DIFFRACTIONr_gen_planes_other0.0070.029
X-RAY DIFFRACTIONr_mcbond_it0.1320.575495
X-RAY DIFFRACTIONr_mcangle_it0.2340.862617
X-RAY DIFFRACTIONr_scbond_it0.1920.621601
LS refinement shellResolution: 1.83→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 34 -
Rwork0.232 684 -
all-718 -
obs--99.45 %
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)
19.24142.9524-1.03322.70862.37144.3156-0.4560.1679-0.6886-0.09890.08150.12260.03030.07710.37440.1387-0.02990.1180.15060.16380.4575-1.289934.589413.0498
212.1848-5.86182.09133.3814-1.73381.30290.24510.0421-0.177-0.1169-0.06440.19490.04720.0617-0.18080.26130.03440.01810.19690.03320.210212.649725.156124.4974
32.3726-0.02120.47284.685-0.14051.7008-0.2547-0.2390.09130.306-0.0023-0.4804-0.12420.08330.25690.06970.0065-0.0390.08510.00950.09115.71544.003617.818
48.7127-1.93480.93576.1238-1.38564.14620.00730.4114-0.1173-0.3880.25940.92890.457-0.4518-0.26670.1577-0.0809-0.03970.14180.0440.156-0.684840.64763.7154
55.3398-1.40370.9843.6245-0.18851.2539-0.0116-0.2605-0.27680.20270.08450.25730.18650.1077-0.07290.07770.02210.01670.05880.00830.027912.300333.609419.2697
65.7205-8.3784.542612.4304-5.100218.78160.26350.0637-0.1082-0.2949-0.05830.13270.66070.1625-0.20520.13230.00390.03910.0750.03060.115519.059131.452513.1318
72.6069-0.21910.73022.3642-1.20492.5468-0.04790.00330.1549-0.058-0.0921-0.34120.06810.25830.14010.0771-0.0010.03320.0576-0.00490.070617.470343.43686.8064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 49
2X-RAY DIFFRACTION2A50 - 59
3X-RAY DIFFRACTION3A60 - 88
4X-RAY DIFFRACTION4A89 - 103
5X-RAY DIFFRACTION5A104 - 121
6X-RAY DIFFRACTION6A122 - 127
7X-RAY DIFFRACTION7A128 - 166

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