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- PDB-6eg2: Crystal structure of human BRM in complex with compound 16 -

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Basic information

Entry
Database: PDB / ID: 6eg2
TitleCrystal structure of human BRM in complex with compound 16
ComponentsMaltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2
KeywordsHydrolase/Hydrolase Inhibitor / Helicase / ATPase / Chromatin remodeling / inhibitor / MBP fusion / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / intermediate filament cytoskeleton / regulation of nucleotide-excision repair / SWI/SNF complex ...bBAF complex / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / intermediate filament cytoskeleton / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / spermatid development / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / helicase activity / negative regulation of cell growth / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nervous system development / outer membrane-bounded periplasmic space / histone binding / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Tandem AAA-ATPase domain / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...Tandem AAA-ATPase domain / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-J7J / Maltose/maltodextrin-binding periplasmic protein / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsZhu, X. / Kulathila, R. / Hu, T. / Xie, X.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers.
Authors: Papillon, J.P.N. / Nakajima, K. / Adair, C.D. / Hempel, J. / Jouk, A.O. / Karki, R.G. / Mathieu, S. / Mobitz, H. / Ntaganda, R. / Smith, T. / Visser, M. / Hill, S.E. / Hurtado, F.K. / ...Authors: Papillon, J.P.N. / Nakajima, K. / Adair, C.D. / Hempel, J. / Jouk, A.O. / Karki, R.G. / Mathieu, S. / Mobitz, H. / Ntaganda, R. / Smith, T. / Visser, M. / Hill, S.E. / Hurtado, F.K. / Chenail, G. / Bhang, H.C. / Bric, A. / Xiang, K. / Bushold, G. / Gilbert, T. / Vattay, A. / Dooley, J. / Costa, E.A. / Park, I. / Li, A. / Farley, D. / Lounkine, E. / Yue, Q.K. / Xie, X. / Zhu, X. / Kulathila, R. / King, D. / Hu, T. / Vulic, K. / Cantwell, J. / Luu, C. / Jagani, Z.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.title
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2524
Polymers69,6531
Non-polymers5993
Water543
1
A: Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2
hetero molecules

A: Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5048
Polymers139,3062
Non-polymers1,1986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3700 Å2
ΔGint1 kcal/mol
Surface area56360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.790, 136.790, 120.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / ATP-dependent helicase ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 69653.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, SMARCA2, BAF190B, BRM, SNF2A, SNF2L2
Production host: Escherichia coli
References: UniProt: P0AEY0, UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-J7J / N-(5-amino-2-chloropyridin-4-yl)-N'-(4-bromo-3-{[3-(hydroxymethyl)phenyl]ethynyl}-1,2-thiazol-5-yl)urea


Mass: 478.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13BrClN5O2S
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Hepes pH7.5, 200mM sodium chloride, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→120.688 Å / Num. obs: 23436 / % possible obs: 97.9 % / Redundancy: 12.7 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.98→2.99 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQA, 5HZR

1fqa

5hzr


Resolution: 2.98→96.73 Å / Cor.coef. Fo:Fc: 0.8518 / Cor.coef. Fo:Fc free: 0.8471 / SU R Cruickshank DPI: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.851 / SU Rfree Blow DPI: 0.41 / SU Rfree Cruickshank DPI: 0.418
RfactorNum. reflection% reflectionSelection details
Rfree0.3037 1155 4.94 %RANDOM
Rwork0.2511 ---
obs0.2536 23393 97.49 %-
Displacement parametersBiso max: 189.41 Å2 / Biso mean: 102.83 Å2 / Biso min: 36.11 Å2
Baniso -1Baniso -2Baniso -3
1-23.5649 Å20 Å20 Å2
2--23.5649 Å20 Å2
3----47.1297 Å2
Refine analyzeLuzzati coordinate error obs: 0.552 Å
Refinement stepCycle: final / Resolution: 2.98→96.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 36 3 4933
Biso mean--100.4 57.44 -
Num. residues----619
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1735SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes714HARMONIC5
X-RAY DIFFRACTIONt_it5047HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion655SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5869SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5047HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6847HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion22.76
LS refinement shellResolution: 2.98→3.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.4135 120 4.28 %
Rwork0.2928 2685 -
all0.2977 2805 -
obs--97.73 %

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