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- PDB-6v1b: Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 -

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Basic information

Entry
Database: PDB / ID: 6v1b
TitleCrystal structure of the bromodomain of human BRD9 bound to I-BRD9
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / BRD9 / mSWI/SNF / BAF / non-BET / BRD / Rhabdomyosarcoma antigen / I-BRD9 / IBRD9
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-H1B / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKarim, M.R. / Chan, A. / 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 20, 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: 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

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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)29,5575
Polymers28,5002
Non-polymers1,0573
Water5,639313
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8093
Polymers14,2501
Non-polymers5602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7472
Polymers14,2501
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Bromodomain-containing protein 9
hetero molecules

B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5575
Polymers28,5002
Non-polymers1,0573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.990, 38.500, 60.920
Angle α, β, γ (deg.)90.000, 108.990, 90.000
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: 14249.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: I-BRD9 / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9H8M2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-H1B / N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide


Mass: 497.554 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H22F3N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KSCN, 30% w/v PEG MME 2,000

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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: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→57.61 Å / Num. obs: 53866 / % possible obs: 97.4 % / Redundancy: 3.73 % / Biso Wilson estimate: 25.997 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 1.061 / Net I/σ(I): 12.83 / Num. measured all: 200920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.393.750.5711.9814836408039560.8590.66797
1.39-1.423.6790.492.2914072394438250.8860.57497
1.42-1.463.5340.3513.0513199386937350.9350.41696.5
1.46-1.513.5890.2454.2412725367935460.9670.28996.4
1.51-1.563.8650.2085.513937365736060.9770.24298.6
1.56-1.613.8560.1796.513254349934370.9820.20898.2
1.61-1.673.830.1497.9712920344833730.9860.17397.8
1.67-1.743.80.1269.6312099323231840.9890.14798.5
1.74-1.823.7470.10711.4711477312830630.9910.12597.9
1.82-1.913.6860.08114.2110806301329320.9930.09597.3
1.91-2.013.3710.06416.549095284626980.9940.07794.8
2.01-2.133.7920.05520.8110038269826470.9960.06498.1
2.13-2.283.9090.04923.449906255525340.9960.05799.2
2.28-2.463.8780.04525.099083236623420.9960.05299
2.46-2.73.8060.04426.258125216121350.9960.05298.8
2.7-3.023.7350.04227.557324200219610.9970.04898
3.02-3.493.6110.03728.346091174816870.9970.04496.5
3.49-4.273.5610.03529.235089150914290.9970.04294.7
4.27-6.043.9640.03531.014586117011570.9980.04198.9
6.04-57.613.6480.03329.622586776190.9970.03891.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UZF

6uzf


Resolution: 1.35→57.61 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.54
RfactorNum. reflection% reflection
Rfree0.2025 1077 2 %
Rwork0.1827 --
obs0.1831 53861 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.7 Å2 / Biso mean: 34.3932 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.35→57.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 120 313 2280
Biso mean--29.6 36.37 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.410.35761330.35466508664197
1.41-1.490.29521330.32856490662396
1.49-1.580.27031340.24416581671598
1.58-1.70.32041340.22436598673298
1.7-1.870.26131360.21066621675798
1.87-2.140.21271330.18326553668697
2.14-2.70.18911370.17246717685499
2.7-57.610.16291370.15436716685397

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