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- PDB-5i7y: BRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dih... -

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Basic information

Entry
Database: PDB / ID: 5i7y
TitleBRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / BRD9 / bromodomain / epigenetics / structure-based design
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 / chromatin / positive regulation of cell population proliferation / 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 / chromatin / positive regulation of cell population proliferation / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-69G / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4514 Å
AuthorsMurray, J.M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.
Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / ...Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / Kiefer, J.R. / Jiang, Y. / Murray, J. / Nasveschuk, C.G. / Pardo, E. / Poy, F. / Romero, F.A. / Tang, Y. / Wang, J. / Xu, Z. / Zawadzke, L.E. / Zhu, X. / Albrecht, B.K. / Magnuson, S.R. / Bellon, S. / Cochran, A.G.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0632
Polymers11,7281
Non-polymers3351
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.636, 33.955, 39.489
Angle α, β, γ (deg.)66.860, 74.850, 73.560
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11727.741 Da / Num. of mol.: 1
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-69G / 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 18460 / % possible obs: 94.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 21.76 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.033 / Rrim(I) all: 0.056 / Χ2: 1.147 / Net I/av σ(I): 25.724 / Net I/σ(I): 10.5 / Num. measured all: 53109
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.45-1.52.60.468185
1.5-1.562.70.356191.6
1.56-1.632.90.29194.6
1.63-1.722.90.217194.5
1.72-1.8330.15195.6
1.83-1.972.90.096195.4
1.97-2.1730.063195.6
2.17-2.482.90.049196
2.48-3.122.90.037195.8
3.12-102.90.029196.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4514→23.284 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.1873 912 4.97 %
Rwork0.1544 --
obs0.1561 18332 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.92 Å2 / Biso mean: 29.4646 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: final / Resolution: 1.4514→23.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 26 115 955
Biso mean--32.25 39.87 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005863
X-RAY DIFFRACTIONf_angle_d0.6691163
X-RAY DIFFRACTIONf_chiral_restr0.061120
X-RAY DIFFRACTIONf_plane_restr0.004149
X-RAY DIFFRACTIONf_dihedral_angle_d13.033317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4514-1.52790.27421100.20732185229582
1.5279-1.62360.23591300.18492489261993
1.6236-1.74890.28261300.16912526265695
1.7489-1.92480.19181330.14652549268295
1.9248-2.20320.17511440.1362522266696
2.2032-2.7750.19991410.1672578271996
2.775-23.28660.16631240.14842571269596

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