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- PDB-7td9: G-059 bound to the SMARCA4 (BRG1) Bromodomain -

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Basic information

Entry
Database: PDB / ID: 7td9
TitleG-059 bound to the SMARCA4 (BRG1) Bromodomain
ComponentsIsoform 4 of Transcription activator BRG1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bromodomain BRG1 SMARCA4 inhibitor / protein binding / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyHydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 4-phenyl-5H-pyridazino[4,3-b]indol-3-amine / Isoform 4 of Transcription activator BRG1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsTang, Y. / Poy, F. / Taylor, A.M. / Cochran, A.G. / Bellon, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1.
Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, ...Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, S. / Leblanc, Y. / Murray, J. / Nasveschuk, C.G. / Neiss, A. / Poy, F. / Romero, F.A. / Sandy, P. / Tang, Y. / Tsui, V. / Zawadzke, L. / Sims 3rd, R.J. / Audia, J.E. / Bellon, S.F. / Magnuson, S.R. / Albrecht, B.K. / Cochran, A.G.
History
DepositionDec 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
AAA: Isoform 4 of Transcription activator BRG1
BBB: Isoform 4 of Transcription activator BRG1
CCC: Isoform 4 of Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0946
Polymers45,3133
Non-polymers7813
Water4,125229
1
AAA: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.260, 90.260, 96.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53BBB
63CCC

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAAAA1452 - 15647 - 119
211SERSERILEILEBBBB1452 - 15647 - 119
322LYSLYSLYSLYSAAAA1450 - 15635 - 118
422LYSLYSLYSLYSCCCC1450 - 15635 - 118
533SERSERLYSLYSBBBB1452 - 15637 - 118
633SERSERLYSLYSCCCC1452 - 15637 - 118

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Isoform 4 of Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 15104.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Two N-terminus residues "GS" are vector-derived residues.
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532-4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GJN / 4-phenyl-5H-pyridazino[4,3-b]indol-3-amine


Mass: 260.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H12N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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 %
Description: Very thin plates that nonetheless diffract to extreme high resolution.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM) Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at ...Details: Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM) Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at 0.1 M, 5% v/v Ethyl acetate
PH range: 8.2-8.8 / Temp details: 4 degree Celsius

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 57838 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.044 / Net I/σ(I): 9.9 / Num. measured all: 538312
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.61-1.679.40.84457411.0011100
1.67-1.739.50.62457731.0421100
1.73-1.819.50.45957531.0771100
1.81-1.919.50.3257701.0651100
1.91-2.039.50.21457591.0221100
2.03-2.199.50.14357791.0541100
2.19-2.49.40.10157841.0271100
2.4-2.759.20.157981.081100
2.75-3.4790.06658131.031100
3.47-508.60.04658681.049199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.15 Å
Translation2.5 Å41.15 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TAB

7tab


Resolution: 1.61→41.147 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.434 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.095 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2422 2933 5.079 %
Rwork0.2063 54814 -
all0.208 --
obs-57747 99.874 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.058 Å20.029 Å20 Å2
2--0.058 Å2-0 Å2
3----0.189 Å2
Refinement stepCycle: LAST / Resolution: 1.61→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 60 229 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122990
X-RAY DIFFRACTIONr_angle_refined_deg1.961.6784021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58822.549153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7431521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022181
X-RAY DIFFRACTIONr_nbd_refined0.2130.21388
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2181
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.210
X-RAY DIFFRACTIONr_mcbond_it2.4482.6221398
X-RAY DIFFRACTIONr_mcangle_it3.1993.9191742
X-RAY DIFFRACTIONr_scbond_it4.1163.0461592
X-RAY DIFFRACTIONr_scangle_it5.9224.3762279
X-RAY DIFFRACTIONr_lrange_it6.60635.9874799
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.053693
X-RAY DIFFRACTIONr_ncsr_local_group_20.1370.053631
X-RAY DIFFRACTIONr_ncsr_local_group_30.1360.053585
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.117950.05007
12BBBX-RAY DIFFRACTIONLocal ncs0.117950.05007
23AAAX-RAY DIFFRACTIONLocal ncs0.13690.05007
24CCCX-RAY DIFFRACTIONLocal ncs0.13690.05007
35BBBX-RAY DIFFRACTIONLocal ncs0.135980.05007
36CCCX-RAY DIFFRACTIONLocal ncs0.135980.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.61-1.6520.2021930.17440300.17542450.9360.94599.48170.163
1.652-1.6970.1962290.17439390.17541700.9420.94799.9520.16
1.697-1.7460.2141910.17238000.17439930.940.94999.94990.157
1.746-1.80.2422010.19137380.19339450.9140.93699.84790.172
1.8-1.8590.2282060.19335940.19538060.9220.93499.84240.176
1.859-1.9240.2582010.21134730.21436780.9120.92399.89120.197
1.924-1.9960.2392060.21333440.21535520.9160.92899.94370.206
1.996-2.0770.2351570.21432570.21534140.9280.9361000.209
2.077-2.170.2631560.21831220.22132790.9110.92899.96950.217
2.17-2.2750.2591740.21329650.21531420.910.92899.90450.215
2.275-2.3980.2791570.21128200.21529810.9020.9299.86580.22
2.398-2.5430.2731610.21826620.22128240.9150.9399.96460.237
2.543-2.7180.2751170.2325410.23226580.9170.9291000.261
2.718-2.9340.2471240.23123630.23224890.9270.92699.91960.264
2.934-3.2130.2471050.23121630.23222700.9210.92499.91190.27
3.213-3.5890.234960.2219730.22120720.9370.93899.85520.254
3.589-4.1390.218910.18317480.18418390.9430.9571000.219
4.139-5.0570.223630.17914910.18115540.9430.9571000.226
5.057-7.0980.253650.20911420.21212080.950.95399.91720.264
7.098-41.1470.214400.1836490.1846980.9590.96398.71060.243

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