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- PDB-2h60: Solution Structure of Human Brg1 Bromodomain -

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Basic information

Entry
Database: PDB / ID: 2h60
TitleSolution Structure of Human Brg1 Bromodomain
ComponentsProbable global transcription activator SNF2L4
KeywordsTRANSCRIPTION / ALFA HELIX
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)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
Model type detailsminimized average
AuthorsShen, W. / Xu, C. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: Biochemistry / Year: 2007
Title: Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails
Authors: Shen, W. / Xu, C. / Huang, W. / Zhang, J. / Carlson, J.E. / Tu, X. / Wu, J. / Shi, Y.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)15,1881
Polymers15,1881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Probable global transcription activator SNF2L4 / brahma-related gene 1 Protein / Brg1 / ATP- dependent helicase SMARCA4 / SNF2-beta / BRG-1 protein ...brahma-related gene 1 Protein / Brg1 / 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: 15188.442 Da / Num. of mol.: 1 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: 1mM Brg1 bromodomain U-15N, 13C; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.3Delaglioprocessing
CNS1.1Brungerrefinement
Sparky3.11Goddarddata analysis
RasMol2.6.4Sayledata analysis
MOLMOL2K.2Koradidata analysis
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 1355 restraints, 1132 are NOE-derived distance constraints, 172 dihedral angle restraints,51 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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