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- PDB-5bt4: Crystal structure of BRD4 first bromodomain in complex with SGC-C... -

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Basic information

Entry
Database: PDB / ID: 5bt4
TitleCrystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / chromatin and transcription regulator / acetylation / Structural Genomics / 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
Chem-2LO / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of BRD4 first bromodomain in complex with a 3,5-dimethylisoxazol ligand
Authors: Tallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9498
Polymers45,2983
Non-polymers1,6515
Water6,233346
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6703
Polymers15,0991
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6703
Polymers15,0991
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6082
Polymers15,0991
Non-polymers5091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.923, 91.801, 113.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 Da / Num. of mol.: 3 / Fragment: UNP residues 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Details (production host): LIC-cloning / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: O60885
#2: Chemical ChemComp-2LO / 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole


Mass: 509.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H33ClN4O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density meas: 437817.563 Mg/m3 / Density % sol: 49.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M succinic acid, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→71.44 Å / Num. all: 695346 / Num. obs: 71462 / % possible obs: 99.6 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.098 / Rsym value: 0.034 / Net I/av σ(I): 4.8 / Net I/σ(I): 14.4
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.8 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→71.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.24 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21425 3567 5 %RANDOM
Rwork0.1912 ---
obs0.19235 67816 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.5→71.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 116 346 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023370
X-RAY DIFFRACTIONr_bond_other_d0.0030.023213
X-RAY DIFFRACTIONr_angle_refined_deg1.4222.0134588
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0147429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04325.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88815584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.249159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7731.2341505
X-RAY DIFFRACTIONr_mcbond_other0.7721.2321504
X-RAY DIFFRACTIONr_mcangle_it1.2491.8451873
X-RAY DIFFRACTIONr_mcangle_other1.2481.8471874
X-RAY DIFFRACTIONr_scbond_it1.3241.461865
X-RAY DIFFRACTIONr_scbond_other1.3231.461865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.112.1282715
X-RAY DIFFRACTIONr_long_range_B_refined4.2711.4944309
X-RAY DIFFRACTIONr_long_range_B_other4.27111.4984310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.497→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 231 -
Rwork0.204 4721 -
obs--95.18 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.7518-0.3220.01050.5232-0.10650.0364-0.0271-0.016-0.00710.01940.031-0.0148-0.0058-0.012-0.00390.01250.0105-0.0020.0240.00070.0158Chain A24.443671.181816.84
20.1128-0.25340.03620.7649-0.25770.2626-0.03120.00650.0110.04350.0087-0.00420.0061-0.02080.02240.0160.0009-0.01020.01450.00330.0294Chain B24.367347.5617-0.3487
30.7195-0.6896-0.48820.910.57420.72730.0025-0.08360.0445-0.05080.062-0.0529-0.0170.0695-0.06450.0426-0.00330.0110.0136-0.00810.0083Chain C40.009226.249718.7845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 168
2X-RAY DIFFRACTION2B1 - 167
3X-RAY DIFFRACTION3C44 - 167

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