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- PDB-6v0x: Crystal structure of the bromodomain of human BRD9 bound to sunitinib -

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Basic information

Entry
Database: PDB / ID: 6v0x
TitleCrystal structure of the bromodomain of human BRD9 bound to sunitinib
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / Sunitinib / BRD9 / mSWI/SNF / BAF / non-BET / BRD
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-B49 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKarim, M.R. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.
Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6482
Polymers14,2501
Non-polymers3981
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.530, 112.062, 30.823
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.: 1
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 BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9H8M2
#2: Chemical ChemComp-B49 / N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide / SUNITINIB


Mass: 398.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27FN4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→32.53 Å / Num. obs: 18344 / % possible obs: 97.9 % / Redundancy: 13.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Net I/σ(I): 22.6 / Num. measured all: 239696 / Scaling rejects: 350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5313.33.237113208490.8890.9133.366395.2
8.22-32.5310.30.02715521500.9990.0090.02953.198.3

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_3260refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UZF

6uzf


Resolution: 1.5→31.241 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 932 5.09 %
Rwork0.1971 17373 -
obs0.1984 18305 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.99 Å2 / Biso mean: 38.164 Å2 / Biso min: 18.75 Å2
Refinement stepCycle: final / Resolution: 1.5→31.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 29 91 927
Biso mean--36.86 41.58 -
Num. residues----99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.57910.25731250.2239237896
1.5791-1.67810.24251260.2119243297
1.6781-1.80760.22941330.2103245897
1.8076-1.98950.21551320.1989245398
1.9895-2.27730.21441360.185250198
2.2773-2.86880.23561340.2142247896
2.8688-31.2410.21751460.1896267398
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)
12.16630.03680.36055.32661.47012.6822-0.0324-0.121-0.19350.22410.11340.81250.493-0.20110.02020.2379-0.0289-0.01670.21450.06610.2899-13.549113.8763-2.9087
26.1671-4.00340.53945.2462.87734.0571-0.16820.35650.2752-0.5896-0.135-0.3205-0.09060.33590.1680.2725-0.06210.04760.32520.00350.29560.389329.8138-4.892
34.46651.08770.12844.2665-0.58652.2339-0.26450.4459-0.3706-0.72310.28280.03220.2277-0.047-0.06070.2382-0.02750.04410.1627-0.00310.1829-5.740815.878-7.0191
43.29763.13182.97413.86224.26076.73040.1698-0.1764-0.66670.8231-0.01260.08781.1049-0.0616-0.16620.44730.02480.060.32750.10670.5029-3.100711.19863.9121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 54 )A22 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 60 )A55 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 104 )A61 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 120 )A105 - 120

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