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- PDB-6v0s: Crystal structure of the bromodomain of human BRD9 bound to TG003 -

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Basic information

Entry
Database: PDB / ID: 6v0s
TitleCrystal structure of the bromodomain of human BRD9 bound to TG003
ComponentsBromodomain-containing protein 9
KeywordsGENE REGULATION / BRD9 / mSWI/SNF / BAF / non-BET / BRD / TG003
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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EAE / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)28,9984
Polymers28,5002
Non-polymers4992
Water1267
1
A: Bromodomain-containing protein 9
hetero molecules

B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9984
Polymers28,5002
Non-polymers4992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1810 Å2
ΔGint-11 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.634, 123.013, 31.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 138 - 250 / Label seq-ID: 11 - 123

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q9H8M2
#2: Chemical ChemComp-EAE / (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one


Mass: 249.329 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C13H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2 M Li2SO4, 0.1 M HEPES (pH 7.5), 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2017
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→74.63 Å / Num. obs: 12097 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.011 / Rrim(I) all: 0.036 / Net I/σ(I): 37.4 / Num. measured all: 128464 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.4-2.4910.90.3161356812420.9930.10.3327.6
8.98-74.638.30.022243429310.0080.02483.2

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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: 3HME

3hme


Resolution: 2.4→37.317 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.33
RfactorNum. reflection% reflection
Rfree0.2301 600 5 %
Rwork0.1923 --
obs0.1942 12005 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.63 Å2 / Biso mean: 79.3364 Å2 / Biso min: 44.53 Å2
Refinement stepCycle: final / Resolution: 2.4→37.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 34 7 1879
Biso mean--67.53 59.41 -
Num. residues----226
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1104X-RAY DIFFRACTION9.405TORSIONAL
12B1104X-RAY DIFFRACTION9.405TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.64150.32491460.2569278699
2.6415-3.02360.35291450.2632277599
3.0236-3.80880.26771500.21652830100
3.8088-37.3170.17951590.15863014100
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)
13.37022.7202-0.92543.5997-3.16794.7757-0.16410.207-0.37590.0063-0.3648-0.73320.5224-0.01690.53490.57380.07530.15570.5493-0.02440.6434-13.40411.0375-9.8035
25.0382-0.6575-0.30266.79750.29121.00160.1712-0.39520.35061.0589-0.21010.65440.1309-0.05070.01680.63860.00610.23340.5732-0.11270.6629-20.331920.728-5.7342
36.13732.3782-0.00932.5782-1.75161.9064-0.21850.1874-0.39320.02680.49421.24970.4437-0.5994-0.19660.50270.02580.14990.6007-0.05210.7644-24.18528.5741-15.5098
47.3294-7.524-5.73728.68984.89726.8114-0.5008-0.269-0.70410.64710.09690.74870.67820.14780.50010.6507-0.0658-0.09670.5387-0.01440.81897.44278.8082-6.6041
59.2333-2.60770.57946.8718-0.26972.84510.01840.17870.97640.22760.0836-0.5774-0.0338-0.128-0.0790.4157-0.0677-0.09180.43240.0240.61496.546221.6027-12.2004
65.0415-3.8440.51445.6948-1.25971.19650.1183-0.69830.67150.50740.1431-0.9278-0.25730.1464-0.13680.9496-0.0734-0.30540.7567-0.18510.758412.517917.37420.241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 49 )A22 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 104 )A50 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 134 )A105 - 134
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 44 )B22 - 44
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 99 )B45 - 99
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 134 )B100 - 134

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