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- PDB-2grc: 1.5 A structure of bromodomain from human BRG1 protein, a central... -

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Basic information

Entry
Database: PDB / ID: 2grc
Title1.5 A structure of bromodomain from human BRG1 protein, a central ATPase of SWI/SNF remodeling complex
ComponentsProbable global transcription activator SNF2L4
KeywordsHYDROLASE / Bromodomain / BRG1 / chromatin remodelling / acely-lysine binding / protein-protein interactions
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex ...positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / RSC-type complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / regulation of G0 to G1 transition / RNA polymerase I preinitiation complex assembly / Tat protein binding / host-mediated activation of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / nuclear androgen receptor binding / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / lncRNA binding / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / positive regulation of signal transduction by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / Chromatin modifying enzymes / DNA polymerase binding / helicase activity / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / negative regulation of cell growth / positive regulation of miRNA transcription / Negative Regulation of CDH1 Gene Transcription / fibrillar center / Formation of the beta-catenin:TCF transactivating complex / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / RMTs methylate histone arginines / p53 binding / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / nucleoplasm / extracellular region / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, 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 / QLQ / Glutamine-Leucine-Glutamine, 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
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 / MAD / Resolution: 1.5 Å
AuthorsSingh, M. / Popowicz, G.M. / Krajewski, M. / Holak, T.A.
CitationJournal: Chembiochem / Year: 2007
Title: Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex.
Authors: Singh, M. / Popowicz, G.M. / Krajewski, M. / Holak, T.A.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable global transcription activator SNF2L4


Theoretical massNumber of molelcules
Total (without water)15,0911
Polymers15,0911
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.860, 30.330, 66.820
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

#1: Protein Probable global transcription activator SNF2L4 / ATP- dependent helicase SMARCA4 / SNF2-beta / BRG-1 protein / Mitotic growth and transcription ...ATP- dependent helicase SMARCA4 / SNF2-beta / BRG-1 protein / Mitotic growth and transcription activator / Brahma protein homolog 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 15091.295 Da / Num. of mol.: 1 / Fragment: bromodomain, residues 1448-1575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BRG1, SNF2B, SNF2L4 / Plasmid: pET46LIC/EK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris, 25% w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05, 0.9793, 0.9796, 0.9770
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2005
RadiationMonochromator: DESY BW6 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.97931
30.97961
40.9771
ReflectionResolution: 1.5→27.62 Å / Num. obs: 18402
Reflection shellResolution: 1.5→1.539 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→27.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.901 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26399 987 5.1 %RANDOM
Rwork0.24217 ---
all0.25 ---
obs0.24333 18402 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.22 Å2
2--0.24 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 165 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022997
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9971340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1995120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49725.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63815204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.548155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02727
X-RAY DIFFRACTIONr_nbd_refined0.2250.2546
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.222
X-RAY DIFFRACTIONr_mcbond_it1.0661.5627
X-RAY DIFFRACTIONr_mcangle_it1.5292993
X-RAY DIFFRACTIONr_scbond_it2.3543411
X-RAY DIFFRACTIONr_scangle_it3.54.5347
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 73 -
Rwork0.298 1332 -
obs--99.93 %

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