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- PDB-9c4b: Second BAF53a of the human TIP60 complex -

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Basic information

Entry
Database: PDB / ID: 9c4b
TitleSecond BAF53a of the human TIP60 complex
ComponentsActin-like protein 6A
KeywordsGENE REGULATION / Chromatin Modification
Function / homology
Function and homology information


regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / neural retina development / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / Ino80 complex / blastocyst formation / RSC-type complex ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / neural retina development / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / Ino80 complex / blastocyst formation / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / spinal cord development / regulation of chromosome organization / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / negative regulation of cell differentiation / positive regulation of myoblast differentiation / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / telomere maintenance / positive regulation of DNA repair / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA Damage Recognition in GG-NER / kinetochore / RMTs methylate histone arginines / nuclear matrix / UCH proteinases / nervous system development / nucleosome / HATs acetylate histones / regulation of apoptotic process / DNA recombination / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / signal transduction / protein-containing complex / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Actin, conserved site / Actins signature 2. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin-like protein 6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYang, Z. / Mameri, A. / Florez Ariza, A.J. / Cote, J. / Nogales, E.
Funding support United States, Canada, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Canadian Institutes of Health Research (CIHR) Canada
Canada Research Chairs Canada
CitationJournal: Science / Year: 2024
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 nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) ...The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) 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
DepositionJun 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.2Sep 11, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-like protein 6A


Theoretical massNumber of molelcules
Total (without water)47,5101
Polymers47,5101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A, INO80K / Production host: Homo sapiens (human) / References: UniProt: O96019

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Second BAF53a of the human TIP60 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: 4D-STEM / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96931 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033144
ELECTRON MICROSCOPYf_angle_d0.5194267
ELECTRON MICROSCOPYf_dihedral_angle_d5.042424
ELECTRON MICROSCOPYf_chiral_restr0.042475
ELECTRON MICROSCOPYf_plane_restr0.004553

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