- EMDB-37988: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state -
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Entry
Database: EMDB / ID: EMD-37988
Title
Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Map data
Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Sample
Complex: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Protein or peptide: x 14 types
DNA: x 2 types
Ligand: x 4 types
Keywords
Remodeler / SRCAP / H2A.Z / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
positive regulation of lymphoid progenitor cell differentiation / ATP-dependent H2AZ histone chaperone activity / modification-dependent protein binding / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport ...positive regulation of lymphoid progenitor cell differentiation / ATP-dependent H2AZ histone chaperone activity / modification-dependent protein binding / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / histone chaperone activity / establishment of protein localization to chromatin / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / R2TP complex / postsynaptic actin cytoskeleton / dynein axonemal particle / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / heart process / RPAP3/R2TP/prefoldin-like complex / GBAF complex / dense body / Formation of annular gap junctions / Swr1 complex / regulation of G0 to G1 transition / neural retina development / muscle cell differentiation / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Ino80 complex / nucleolus organization / Activation of the TFAP2 (AP-2) family of transcription factors / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / Adherens junctions interactions / Telomere Extension By Telomerase / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / protein folding chaperone complex / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / negative regulation of transcription by RNA polymerase I / positive regulation of T cell differentiation / apical junction complex / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / maintenance of blood-brain barrier / cortical cytoskeleton / regulation of chromosome organization / positive regulation of stem cell population maintenance / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / somatic stem cell population maintenance / calyx of Held / TFIID-class transcription factor complex binding / negative regulation of cell differentiation / regulation of embryonic development / MLL1 complex / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of transcription initiation by RNA polymerase II / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / RHO GTPases Activate WASPs and WAVEs / positive regulation of DNA repair / RHO GTPases activate IQGAPs / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding Similarity search - Function
Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / Zinc finger, HIT-type / : ...Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / Zinc finger, HIT-type / : / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / domain in helicases and associated with SANT domains / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / DNA binding domain with preference for A/T rich regions / HSA domain / AT hook, DNA-binding motif / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Histone-fold / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Zinc finger HIT domain-containing protein 1 / YEATS domain-containing protein 4 / Actin-like protein 6A / Actin, cytoplasmic 1 / Arachidonate 15-lipoxygenase / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Vacuolar protein sorting-associated protein 72 homolog / Helicase SRCAP / Histone H2A type 1-C ...Zinc finger HIT domain-containing protein 1 / YEATS domain-containing protein 4 / Actin-like protein 6A / Actin, cytoplasmic 1 / Arachidonate 15-lipoxygenase / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Vacuolar protein sorting-associated protein 72 homolog / Helicase SRCAP / Histone H2A type 1-C / Actin-related protein 6 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.2 Å
National Natural Science Foundation of China (NSFC)
China
Citation
Journal: Cell Discov / Year: 2024 Title: Structural insights into histone exchange by human SRCAP complex. Authors: Jiali Yu / Fengrui Sui / Feng Gu / Wanjun Li / Zishuo Yu / Qianmin Wang / Shuang He / Li Wang / Yanhui Xu / Abstract: Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with ...Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeF-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.
Name: Helicase SRCAP / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Name: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
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