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- PDB-8xvv: The TRRAP module of human NuA4/TIP60 complex -

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Basic information

Entry
Database: PDB / ID: 8xvv
TitleThe TRRAP module of human NuA4/TIP60 complex
Components
  • Isoform 2 of E1A-binding protein p400
  • Isoform 2 of Transformation/transcription domain-associated protein
KeywordsTRANSCRIPTION / Remodeler / Histone Acetyltransferase Complex / NuA4 / TIP60
Function / homology
Function and homology information


transcription factor TFTC complex / protein antigen binding / Swr1 complex / regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination ...transcription factor TFTC complex / protein antigen binding / Swr1 complex / regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / helicase activity / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / DNA Damage/Telomere Stress Induced Senescence / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle / hydrolase activity / Ub-specific processing proteases / nuclear speck / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain ...E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / PIK-related kinase, FAT / FAT domain / FATC / : / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT/Myb domain / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Helicase conserved C-terminal domain / Armadillo-like helical / 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 / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / E1A-binding protein p400 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen, K. / Wang, L. / Yu, Z. / Yu, J. / Ren, Y. / Wang, Q. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the human TIP60 complex
Authors: Chen, K. / Wang, L. / Yu, Z. / Yu, J. / Ren, Y. / Wang, Q. / Xu, Y.
History
DepositionJan 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Isoform 2 of E1A-binding protein p400
L: Isoform 2 of Transformation/transcription domain-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)775,8083
Polymers775,1482
Non-polymers6601
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 Isoform 2 of E1A-binding protein p400 / CAG repeat protein 32 / Domino homolog / hDomino / Trinucleotide repeat-containing gene 12 protein ...CAG repeat protein 32 / Domino homolog / hDomino / Trinucleotide repeat-containing gene 12 protein / p400 kDa SWI2/SNF2-related protein


Mass: 340198.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP400, CAGH32, KIAA1498, KIAA1818, TNRC12 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q96L91, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Isoform 2 of Transformation/transcription domain-associated protein / 350/400 kDa PCAF-associated factor / PAF350/400 / STAF40 / Tra1 homolog


Mass: 434949.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRRAP, PAF400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y4A5
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: The TRRAP module of human NuA4/TIP60 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190003 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7KTR

7ktr


Accession code: 7KTR / Source name: PDB / Type: experimental model

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