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- PDB-4z6h: Crystal structure of BRD9 bromodomain in complex with a valerolac... -

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Basic information

Entry
Database: PDB / ID: 4z6h
TitleCrystal structure of BRD9 bromodomain in complex with a valerolactam quinolone ligand
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / lysine-acetylated histone binding / chromatin regulator / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4L2 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. ...Tallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor.
Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / ...Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / Brennan, P.E. / Dixon, D.J.
History
DepositionApr 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 9
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0404
Polymers28,5002
Non-polymers5412
Water1,22568
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5202
Polymers14,2501
Non-polymers2701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5202
Polymers14,2501
Non-polymers2701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.233, 125.220, 29.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

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Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: unp residues 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-4L2 / 1,4-dimethyl-7-(2-oxopiperidin-1-yl)quinolin-2(1H)-one


Mass: 270.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.33 Å3/Da / Density meas: 265586.938 Mg/m3 / Density % sol: 47.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M PCB pH 8, 30% PEG1K / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→28.97 Å / Num. all: 25694 / Num. obs: 25694 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.033 / Rsym value: 0.014 / Net I/σ(I): 25.4
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.8→28.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.695 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27084 1283 5 %RANDOM
Rwork0.22071 ---
obs0.22314 24360 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.705 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å2-0 Å2
2---2.6 Å20 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.8→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 40 68 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191923
X-RAY DIFFRACTIONr_bond_other_d0.0020.021888
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9962583
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0054359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.625224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50523.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5071510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
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_it2.7693.046902
X-RAY DIFFRACTIONr_mcbond_other2.7613.047901
X-RAY DIFFRACTIONr_mcangle_it3.6954.5461124
X-RAY DIFFRACTIONr_mcangle_other3.6954.5461125
X-RAY DIFFRACTIONr_scbond_it3.3263.5171021
X-RAY DIFFRACTIONr_scbond_other3.3253.521022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0345.1491460
X-RAY DIFFRACTIONr_long_range_B_refined7.56726.6592278
X-RAY DIFFRACTIONr_long_range_B_other7.57426.572261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å
RfactorNum. reflection% reflection
Rfree0.336 85 -
Rwork0.306 1755 -
obs--98.4 %
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)
10.555-0.174-0.12072.3305-0.49262.1229-0.1387-0.06120.0493-0.01450.02110.0689-0.32690.06340.11750.26840.0031-0.0650.01430.01850.0848Chain A99.13145.67468.0317
22.1892-1.05290.67825.74080.86650.49470.18380.469-0.29210.492-0.06790.12130.20250.2276-0.11590.32380.245-0.02830.3573-0.10020.0514Chain B90.3242179.63285.7984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B22 - 134
2X-RAY DIFFRACTION2B22 - 134

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