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Open data
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Basic information
Entry | Database: PDB / ID: 9c57 | ||||||||||||||||||
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Title | Reconstituted P400 Subcomplex of the human TIP60 complex | ||||||||||||||||||
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![]() | GENE REGULATION / complex / chromatin regulator | ||||||||||||||||||
Function / homology | ![]() ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / 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 / sperm DNA condensation ...ATP-dependent H2AZ histone chaperone activity / piccolo histone acetyltransferase complex / 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 / sperm DNA condensation / 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 / R2TP complex / brahma complex / postsynaptic actin cytoskeleton / dynein axonemal particle / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / chromatin-protein adaptor activity / RPAP3/R2TP/prefoldin-like complex / GBAF complex / protein antigen binding / dense body / Formation of annular gap junctions / Swr1 complex / regulation of G0 to G1 transition / neural retina development / 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 / 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 / tight junction / enzyme-substrate adaptor activity / 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 / apical junction complex / positive regulation of T cell differentiation / establishment or maintenance of cell polarity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of gene expression, epigenetic / spinal cord development / cortical cytoskeleton / maintenance of blood-brain barrier / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / 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 / Telomere Extension By Telomerase / spermatid development / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RNA polymerase II core promoter sequence-specific DNA binding / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / regulation of DNA repair / histone acetyltransferase activity / Deposition of new CENPA-containing nucleosomes at the centromere / EPHB-mediated forward signaling / substantia nigra development Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||||||||||||||
![]() | Yang, Z. / Mameri, A. / Florez Ariza, A.J. / Cote, J. / Nogales, E. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Authors: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie ...Authors: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie Fradet-Turcotte / Jean-Philippe Lambert / Jeff A Ranish / Jacques Côté / Eva Nogales / ![]() ![]() Abstract: The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to regulate ...The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the EP400 subunit serves as a scaffold holding the different functional modules in specific positions, creating a unique arrangement of the ARP module. EP400 interacts with the TRRAP subunit using a footprint that overlaps with that of the SAGA acetyltransferase complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 45206MC ![]() 9c47C ![]() 9c4bC ![]() 9c62C ![]() 9c6nC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 8 types, 13 molecules ECAHMLBDFGIJK
#1: Protein | Mass: 50296.914 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 93589.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 47509.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 51222.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | | Mass: 343867.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q96L91, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #6: Protein | | Mass: 53090.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein | | Mass: 40658.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 2 types, 8 molecules ![](data/chem/img/AGS.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#9: Chemical | ChemComp-AGS / #10: Chemical | ChemComp-ATP / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Reconstituted P400 Subcomplex of the human TIP60 complex Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 4D-STEM / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166442 / Symmetry type: POINT |
Refinement | Cross valid method: NONE |