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- PDB-6zs2: Crystal Structure of the bromodomain of human transcription activ... -

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Basic information

Entry
Database: PDB / ID: 6zs2
TitleCrystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol
ComponentsTranscription activator BRG1
KeywordsGENE REGULATION / BROMODOMAIN / 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 / STRUCTURAL GENOMICS CONSORTIUM / SGC / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / negative regulation of androgen receptor signaling pathway / nBAF complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / negative regulation of androgen receptor signaling pathway / nBAF complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / RSC-type complex / ATP-dependent chromatin remodeler activity / host-mediated activation of viral transcription / regulation of nucleotide-excision repair / nucleosome disassembly / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / 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 / positive regulation of signal transduction by p53 class mediator / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Formation of the beta-catenin:TCF transactivating complex / helicase activity / negative regulation of cell growth / kinetochore / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nuclear matrix / fibrillar center / p53 binding / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
SWI/SNF complex subunit BRG1 / 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 ...SWI/SNF complex subunit BRG1 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-FX5 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsPreuss, F. / Joerger, A.C. / Kraemer, A. / Wanior, M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis.
Authors: Wanior, M. / Preuss, F. / Ni, X. / Kramer, A. / Mathea, S. / Gobel, T. / Heidenreich, D. / Simonyi, S. / Kahnt, A.S. / Joerger, A.C. / Knapp, S.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Transcription activator BRG1
B: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1306
Polymers28,4612
Non-polymers6694
Water4,792266
1
A: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5653
Polymers14,2301
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5653
Polymers14,2301
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.180, 64.910, 48.770
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 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: 14230.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-FX5 / 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol


Mass: 272.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization buffer: 20% medium-molecular-weight PEG smear, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1.57→47.3 Å / Num. obs: 35278 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.1272343356 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.1
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 1915 / CC1/2: 0.973 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKD

5dkd


Resolution: 1.57→34.2487331998 Å / SU ML: 0.14241308346 / Cross valid method: FREE R-VALUE / σ(F): 1.36039202951 / Phase error: 23.1847411695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215317979354 1741 4.94265273677 %
Rwork0.178958143499 33483 -
obs0.180774575223 35224 99.7112608277 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.3242338323 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.2487331998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 48 266 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005320329022592070
X-RAY DIFFRACTIONf_angle_d0.7727816914682792
X-RAY DIFFRACTIONf_chiral_restr0.0457401167629310
X-RAY DIFFRACTIONf_plane_restr0.00404596235641386
X-RAY DIFFRACTIONf_dihedral_angle_d15.66963218931342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.61520.2016707257021410.1729918006452767X-RAY DIFFRACTION99.6914638327
1.6152-1.66730.2106405056151390.171649309652799X-RAY DIFFRACTION99.9319727891
1.6673-1.72690.1906963040941300.1643728525932794X-RAY DIFFRACTION99.9316473001
1.7269-1.7960.1783653563891440.1705603983292792X-RAY DIFFRACTION99.8979244641
1.796-1.87780.2275475719341510.1761097317832780X-RAY DIFFRACTION99.7957099081
1.8778-1.97680.2151505272251260.1892148820782803X-RAY DIFFRACTION99.897680764
1.9768-2.10060.2592748139691550.1799042373942766X-RAY DIFFRACTION99.8974008208
2.1006-2.26280.2203586247851450.1770619869962793X-RAY DIFFRACTION99.8640380693
2.2628-2.49040.2171301223081440.1781509854242803X-RAY DIFFRACTION99.8644527279
2.4904-2.85060.198099261651620.1845815237252769X-RAY DIFFRACTION99.8297002725
2.8506-3.59090.2336574824181500.1859892125172789X-RAY DIFFRACTION99.1231028668
3.5909-34.24873319980.206992867881540.1762770518022828X-RAY DIFFRACTION98.8399071926

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