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- PDB-8a7i: Crystal structure of BRD9 bromodomain in complex with compound EA-89 -

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Basic information

Entry
Database: PDB / ID: 8a7i
TitleCrystal structure of BRD9 bromodomain in complex with compound EA-89
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / Bromodomain / BRD9 / inhibitor
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-L8L / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFaller, M. / Zink, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Blood Cancer J / Year: 2022
Title: BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma.
Authors: Weisberg, E. / Chowdhury, B. / Meng, C. / Case, A.E. / Ni, W. / Garg, S. / Sattler, M. / Azab, A.K. / Sun, J. / Muz, B. / Sanchez, D. / Toure, A. / Stone, R.M. / Galinsky, I. / Winer, E. / ...Authors: Weisberg, E. / Chowdhury, B. / Meng, C. / Case, A.E. / Ni, W. / Garg, S. / Sattler, M. / Azab, A.K. / Sun, J. / Muz, B. / Sanchez, D. / Toure, A. / Stone, R.M. / Galinsky, I. / Winer, E. / Gleim, S. / Gkountela, S. / Kedves, A. / Harrington, E. / Abrams, T. / Zoller, T. / Vaupel, A. / Manley, P. / Faller, M. / Chung, B. / Chen, X. / Busenhart, P. / Stephan, C. / Calkins, K. / Bonenfant, D. / Thoma, C.R. / Forrester, W. / Griffin, J.D.
History
DepositionJun 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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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)27,3224
Polymers26,1322
Non-polymers1,1902
Water3,387188
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6612
Polymers13,0661
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6612
Polymers13,0661
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.083, 66.386, 55.883
Angle α, β, γ (deg.)90, 105.83, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13066.168 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 BL21(DE3) (bacteria) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-L8L / ~{N}-[1,1-bis(oxidanylidene)thian-4-yl]-7-[3-methyl-1-(piperidin-4-ylmethyl)indol-5-yl]-4-oxidanylidene-5-propyl-thieno[3,2-c]pyridine-2-carboxamide


Mass: 594.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H38N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 3350, 0.1M Succinic Acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→53.764 Å / Num. obs: 21364 / % possible obs: 84.54 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.55
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 2507 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YY6

4yy6


Resolution: 1.76→41.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1015 -RANDOM
Rwork0.2007 ---
obs0.2023 21347 84.6 %-
Displacement parametersBiso mean: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.0103 Å20 Å20.9218 Å2
2---8.1795 Å20 Å2
3---7.1692 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.76→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 82 188 1851
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822331HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d557SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1624HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion218SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1608SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion14.95
LS refinement shellResolution: 1.76→1.77 Å
RfactorNum. reflection% reflection
Rfree0.2563 23 -
Rwork0.2466 --
obs0.2472 428 100 %
Refinement TLS params.

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)
11.45150.73150.0382.0225-0.49752.4661-0.0498-0.2434-0.0175-0.24340.09530.1253-0.01750.1253-0.0455-0.0475-0.0092-0.0140.009-0.0255-0.052-3.32132.227811.111
21.5442-0.2657-0.50441.40340.22083.67420.06870.19620.0230.1962-0.0227-0.03120.023-0.0312-0.046-0.0415-0.018-0.021-0.02590.0153-0.036911.1584-3.555133.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A138 - 238
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B138 - 238
4X-RAY DIFFRACTION2{ B|* }B301

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