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Open data
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Basic information
Entry | Database: PDB / ID: 9c4b | |||||||||||||||
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Title | Second BAF53a of the human TIP60 complex | |||||||||||||||
![]() | Actin-like protein 6A | |||||||||||||||
![]() | GENE REGULATION / Chromatin Modification | |||||||||||||||
Function / homology | ![]() regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / neural retina development / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / neural retina development / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / RSC-type complex / blastocyst formation / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / spinal cord development / 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 G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of double-strand break repair via homologous recombination / positive regulation of myoblast differentiation / regulation of DNA repair / positive regulation of DNA repair / telomere maintenance / positive regulation of cell differentiation / DNA Damage Recognition in GG-NER / kinetochore / RMTs methylate histone arginines / nuclear matrix / UCH proteinases / nucleosome / nervous system development / HATs acetylate histones / regulation of apoptotic process / DNA recombination / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / DNA repair / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / signal transduction / protein-containing complex / nucleoplasm / nucleus / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 | ![]() | 153.6 KB | Display | ![]() |
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PDB format | ![]() | 123.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 45180 ![]() 45176 ![]() 9c47C 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
#1: Protein | Mass: 47509.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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: Second BAF53a of the human TIP60 complex / Type: COMPLEX / Entity ID: all / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96931 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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