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- PDB-4flp: Crystal Structure of the first bromodomain of human BRDT in compl... -

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Basic information

Entry
Database: PDB / ID: 4flp
TitleCrystal Structure of the first bromodomain of human BRDT in complex with the inhibitor JQ1
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / BRDT / bromodomain containing protein testis specific / Nucleus / Transcription / Transcription regulation / Structural Genomics Consortium / SGC / Bromodomain / TRANSCRIPTION REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / 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-JQ1 / : / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Qi, J. / Felletar, I. / Canning, P. / Muniz, J. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Picaud, S. / Qi, J. / Felletar, I. / Canning, P. / Muniz, J. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bradner, J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Small-Molecule Inhibition of BRDT for Male Contraception.
Authors: Matzuk, M.M. / McKeown, M.R. / Filippakopoulos, P. / Li, Q. / Ma, L. / Agno, J.E. / Lemieux, M.E. / Picaud, S. / Yu, R.N. / Qi, J. / Knapp, S. / Bradner, J.E.
History
DepositionJun 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 testis-specific protein
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2885
Polymers28,3332
Non-polymers9553
Water1,06359
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6242
Polymers14,1661
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6643
Polymers14,1661
Non-polymers4972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.400, 57.420, 128.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-202-

K

21B-307-

HOH

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Components

#1: Protein Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 14166.427 Da / Num. of mol.: 2 / Fragment: first bromodomain (UNP residues 21-137)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q58F21
#2: Chemical ChemComp-JQ1 / (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium


Mass: 457.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26ClN4O2S / Comment: inhibitor*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M BisTris propane pH 8.0, 0.15M KSCN, 25% PEG3350, 10% EtGly , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 4.1 / Number: 50419 / Rsym value: 0.11 / D res high: 2.2 Å / D res low: 37.4 Å / Num. obs: 14655 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.9637.496.410.0670.0673
4.926.9699.110.0810.0813.2
4.024.929910.0840.0843.1
3.484.029910.0840.0843.5
3.113.4899.410.0880.0883.5
2.843.1199.810.1210.1213.4
2.632.8499.910.1910.1913.5
2.462.6399.910.2870.2873.5
2.322.4699.910.4360.4363.5
2.22.3299.910.6550.6553.6
ReflectionResolution: 2.2→37.4 Å / Num. all: 14729 / Num. obs: 14655 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.323.60.6551.10.655199.9
2.32-2.463.50.4361.70.436199.9
2.46-2.633.50.2872.60.287199.9
2.63-2.843.50.1913.80.191199.9
2.84-3.113.40.1215.70.121199.8
3.11-3.483.50.0886.60.088199.4
3.48-4.023.50.08470.084199
4.02-4.923.10.0846.50.084199
4.92-6.963.20.0816.20.081199.1
6.96-37.430.0676.90.067196.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.93 Å
Translation2.5 Å35.93 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

2rfj

2oss

2ouo

2grc

2oo1

3dai

3d7c

3dwy


Resolution: 2.23→42.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.026 / SU ML: 0.167 / SU R Cruickshank DPI: 0.2648 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25487 708 5 %RANDOM
Rwork0.21113 ---
obs0.21343 13419 99.71 %-
all-14168 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.23→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 63 59 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221881
X-RAY DIFFRACTIONr_bond_other_d0.0010.021234
X-RAY DIFFRACTIONr_angle_refined_deg1.662.0062572
X-RAY DIFFRACTIONr_angle_other_deg0.9233.0013014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59625.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00615317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.536154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
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_it4.1731093
X-RAY DIFFRACTIONr_mcbond_other1.2593421
X-RAY DIFFRACTIONr_mcangle_it6.33551774
X-RAY DIFFRACTIONr_scbond_it9.8478788
X-RAY DIFFRACTIONr_scangle_it11.79911795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 46 -
Rwork0.356 978 -
obs--99.9 %
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)
11.31240.2977-0.41590.9486-0.35160.9864-0.13290.0226-0.16620.01850.0593-0.08790.086-0.03810.07360.04320.00470.02250.1797-0.01040.080710.0889-14.6915-26.5138
20.1063-0.3148-0.24151.5854-0.58313.34290.0510.0435-0.0077-0.1856-0.02810.01180.1909-0.2902-0.02290.1253-0.042-0.04680.248-0.02090.027612.8874-5.7402-53.9038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 134
2X-RAY DIFFRACTION2B29 - 135

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