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- PDB-8ahc: Crystal structure of the BRD9 bromodomain with BI-7189 -

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Basic information

Entry
Database: PDB / ID: 8ahc
TitleCrystal structure of the BRD9 bromodomain with BI-7189
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / Inhibitor / Complex
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-M2O / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.504 Å
AuthorsBader, G. / Boettcher, J. / Weiss-Puxbaum, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Chemmedchem / Year: 2023
Title: Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments.
Authors: Martinelli, P. / Schaaf, O. / Mantoulidis, A. / Martin, L.J. / Fuchs, J.E. / Bader, G. / Gollner, A. / Wolkerstorfer, B. / Rogers, C. / Balikci, E. / Lipp, J.J. / Mischerikow, N. / Doebel, S. ...Authors: Martinelli, P. / Schaaf, O. / Mantoulidis, A. / Martin, L.J. / Fuchs, J.E. / Bader, G. / Gollner, A. / Wolkerstorfer, B. / Rogers, C. / Balikci, E. / Lipp, J.J. / Mischerikow, N. / Doebel, S. / Gerstberger, T. / Sommergruber, W. / Huber, K.V.M. / Bottcher, J.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,1624
Polymers28,5002
Non-polymers6632
Water5,134285
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5812
Polymers14,2501
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5812
Polymers14,2501
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.883, 125.201, 29.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-M2O / [2,6-dimethoxy-4-(1,2,5-trimethyl-6-oxidanylidene-pyridin-3-yl)phenyl]methyl-dimethyl-azanium


Mass: 331.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.44 / Details: 100 mM Tris 28% glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.504→62.6 Å / Num. obs: 25083 / % possible obs: 59.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 1.504→1.672 Å / Num. unique obs: 1254 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5F1H

5f1h


Resolution: 1.504→62.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.121
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1286 5.13 %RANDOM
Rwork0.2111 ---
obs0.2121 25083 59.5 %-
Displacement parametersBiso max: 103.69 Å2 / Biso mean: 41.03 Å2 / Biso min: 15 Å2
Baniso -1Baniso -2Baniso -3
1-1.9158 Å20 Å20 Å2
2---2.5011 Å20 Å2
3---0.5853 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.504→62.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 48 285 2180
Biso mean--29.14 45.98 -
Num. residues----227
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1139SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes586HARMONIC5
X-RAY DIFFRACTIONt_it1950HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3395SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3897HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7065HARMONIC20.76
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion15.29
LS refinement shellResolution: 1.504→1.6 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3721 25 4.98 %
Rwork0.287 477 -
obs--6.92 %
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)
10.8481-0.2007-0.92158.96491.27120.52490.20990.02640.149-0.1392-0.11230.2337-0.0689-0.3005-0.0976-0.05940.0853-0.004-0.0079-0.00540.019716.12368.6995.9446
22.0854-1.75650.28994.9413-0.30341.1439-0.2497-0.0501-0.16960.0540.14030.02410.2923-0.03880.10940.07880.01470.0858-0.0723-0.0108-0.03368.271842.00347.78
30-1.0165-0.01220.1066-0.21570-0.02720.0138-0.2797-0.01920.00830.7037-0.08370.01920.0189-0.0981-0.00680.0180.0263-0.07680.30011.083222.54565.4386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 134
2X-RAY DIFFRACTION2{ B|* }B21 - 134

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