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- PDB-2ouo: Crystal Structure of the Bromo domain 2 in human Bromodomain Cont... -

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Basic information

Entry
Database: PDB / ID: 2ouo
TitleCrystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4)
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN / BRD4 / bromodomain containing protein 4 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsFilippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. ...Filippakopoulos, P. / Keates, T. / Savitsky, P. / Burgess, N. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)15,2474
Polymers15,0601
Non-polymers1863
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.032, 73.698, 33.467
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-78-

HOH

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Components

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


Mass: 15060.332 Da / Num. of mol.: 1 / Fragment: Bromo domain 2
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): Rosetta-R3 / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 11.4 / Number: 44952 / Rmerge(I) obs: 0.065 / Χ2: 1.03 / D res high: 1.89 Å / D res low: 50 Å / Num. obs: 12030 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.075097.710.0441.0293.6
3.234.0798.810.0511.0153.9
2.823.2310010.071.0343.8
2.572.8299.710.0851.0123.8
2.382.5799.810.1151.043.8
2.242.3899.910.1551.073.8
2.132.2499.810.2031.073.8
2.042.1399.310.2941.073.8
1.962.0499.510.4571.0143.7
1.891.9698.610.6180.9413.3
ReflectionResolution: 1.74→73.72 Å / Num. all: 15125 / Num. obs: 15125 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Χ2: 1.031 / Net I/σ(I): 11.4
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.618 / Num. unique all: 1156 / Χ2: 0.941 / % possible all: 98.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å24.77 Å
Translation3.5 Å24.77 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X0J

1x0j


Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.961 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 722 4.8 %RANDOM
Rwork0.182 ---
all0.184 12030 --
obs0.184 12030 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.18 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 12 132 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022934
X-RAY DIFFRACTIONr_bond_other_d0.0050.02649
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9621260
X-RAY DIFFRACTIONr_angle_other_deg1.0483.0031566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57724.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27915162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.097154
X-RAY DIFFRACTIONr_chiral_restr0.090.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
X-RAY DIFFRACTIONr_nbd_refined0.220.2213
X-RAY DIFFRACTIONr_nbd_other0.1830.2622
X-RAY DIFFRACTIONr_nbtor_refined0.180.2461
X-RAY DIFFRACTIONr_nbtor_other0.0890.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.212
X-RAY DIFFRACTIONr_mcbond_it1.0531.5644
X-RAY DIFFRACTIONr_mcbond_other0.3161.5222
X-RAY DIFFRACTIONr_mcangle_it1.4552917
X-RAY DIFFRACTIONr_scbond_it2.1443402
X-RAY DIFFRACTIONr_scangle_it2.9364.5339
LS refinement shellResolution: 1.89→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 41 -
Rwork0.35 933 -
obs-974 87.99 %
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)
13.1157-0.65030.80215.5863-2.00455.55080.01350.08790.3572-0.0842-0.0759-0.2644-0.26370.23950.0624-0.0953-0.02930.0251-0.2450.0154-0.072742.4365.73546.714
21.1229-3.26070.981411.1971-5.43484.72350.05640.2216-0.1526-0.6036-0.2988-0.68270.57850.06460.24240.03640.06450.0788-0.09020.02160.041945.348-16.78747.08
33.58940.8154-0.16793.9052-2.5882.276-0.03010.4459-0.1216-0.60970.012-0.57970.29870.29580.01810.03460.04670.0882-0.18730.0111-0.114442.826-5.41538.886
43.03511.5319-0.94275.2957-3.334.26550.00310.28060.029-0.31870.10810.05230.04610.0162-0.1112-0.00390.01940.0327-0.2734-0.004-0.144335.73-1.50739.576
53.0753-0.5190.2329.3245-0.59342.10640.0483-0.3308-0.1110.5197-0.06820.06890.07740.02370.0199-0.0559-0.01260.0198-0.22520.0085-0.163534.613-3.42552.939
632.1407-6.2182-11.27319.82462.355622.52551.17230.97323.1968-1.0616-0.70530.0217-1.4454-0.688-0.46690.12420.05850.0519-0.17920.11780.214431.68712.7642.395
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11349 - 37719 - 47
22378 - 39048 - 60
33391 - 41061 - 80
44411 - 43181 - 101
55432 - 453102 - 123
66454 - 459124 - 129

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