- EMDB-33684: The nucleosome-bound human PBAF complex -
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Basic information
Entry
Database: EMDB / ID: EMD-33684
Title
The nucleosome-bound human PBAF complex
Map data
PBAF overall map
Sample
Complex: Nucleosome-bound human PBAF complex
Protein or peptide: x 16 types
DNA: x 2 types
Protein or peptide: x 4 types
Ligand: x 3 types
Keywords
chromatin remodeling complexes / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coronary artery morphogenesis / hepatocyte differentiation / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / XY body / RSC-type complex / blastocyst formation / RNA polymerase I preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / germ cell nucleus / positive regulation of double-strand break repair / positive regulation of T cell differentiation / cardiac muscle cell proliferation / cellular response to fatty acid / nuclear androgen receptor binding / negative regulation of G1/S transition of mitotic cell cycle / nuclear chromosome / spinal cord development / homeostatic process / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of Wnt signaling pathway / positive regulation of double-strand break repair via homologous recombination / positive regulation of DNA repair / Packaging Of Telomere Ends / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / embryonic organ development / neurogenesis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Chromatin modifying enzymes / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA polymerase binding / heart morphogenesis / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / histone acetyltransferase activity / Meiotic synapsis / Inhibition of DNA recombination at telomere / transcription coregulator activity / nucleosomal DNA binding / lysine-acetylated histone binding / Regulation of TP53 Activity through Acetylation / RNA Polymerase I Promoter Opening / transcription coregulator binding / Assembly of the ORC complex at the origin of replication / telomere maintenance / Interleukin-7 signaling / DNA methylation / transcription initiation-coupled chromatin remodeling / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / positive regulation of miRNA transcription / negative regulation of cell migration / Defective pyroptosis / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / helicase activity / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / nuclear receptor binding / Transcriptional regulation by small RNAs / positive regulation of cell differentiation / Transcriptional regulation of granulopoiesis Similarity search - Function
PHD finger protein 10 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / RFX DNA-binding domain / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal ...PHD finger protein 10 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / RFX DNA-binding domain / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / : / DNA-binding RFX-type winged-helix domain / SWI/SNF complex subunit BRG1 / RFX-type winged-helix DNA-binding domain profile. / Chromatin-remodeling complex component Sfh1/SNF5 / Protein polybromo-1, Bromodomain 5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Remodelling complex subunit Rsc/polybromo / Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / : / domain in helicases and associated with SANT domains / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / SWIB/MDM2 domain / Bromo adjacent homology (BAH) domain / BAH domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / HMG (high mobility group) box / Chromo/chromo shadow domain / : / Chromatin organization modifier domain / HMG boxes A and B DNA-binding domains profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Actins signature 1. / Actin, conserved site / Actins signature 2. / Centromere kinetochore component CENP-T histone fold / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / BRCT domain superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Histone H2B signature. / Histone H2B / Histone H2B Similarity search - Domain/homology
Histone H3 / ACTB protein / Histone H4 / Actin-like protein 6A / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / AT-rich interactive domain-containing protein 2 / Protein polybromo-1 / SWI/SNF complex subunit SMARCC2 / PHD finger protein 10 ...Histone H3 / ACTB protein / Histone H4 / Actin-like protein 6A / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / AT-rich interactive domain-containing protein 2 / Protein polybromo-1 / SWI/SNF complex subunit SMARCC2 / PHD finger protein 10 / Histone H2A type 1-C / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / Bromodomain-containing protein 7 / Histone H2B Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 4.4 Å
National Natural Science Foundation of China (NSFC)
32030055
China
National Natural Science Foundation of China (NSFC)
China
Citation
Journal: Nat Commun / Year: 2022 Title: Structure of nucleosome-bound human PBAF complex. Authors: Li Wang / Jiali Yu / Zishuo Yu / Qianmin Wang / Wanjun Li / Yulei Ren / Zhenguo Chen / Shuang He / Yanhui Xu / Abstract: BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. ...BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
UniProtKB: AT-rich interactive domain-containing protein 2
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Macromolecule #10: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
Macromolecule
Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Macromolecule #13: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
Macromolecule
Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
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Macromolecule #14: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
Macromolecule
Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
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