+Open data
-Basic information
Entry | Database: PDB / ID: 8qri | ||||||
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Title | TRRAP and EP400 in the human Tip60 complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Eukaryotic transcription / Histone acetyltransferase / chromatin remodeling / Complex | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Li, C. / Smirnova, E. / Schnitzler, C. / Crucifix, C. / Concordet, J.P. / Brion, A. / Poterszman, A. / SChultz, P. / Papai, G. / Ben-Shem, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Nature / Year: 2024 Title: Structure of human TIP60-C histone exchange and acetyltransferase complex Authors: Li, C. / Smirnova, E. / Schnitzler, C. / Crucifix, C. / Concordet, J.P. / Brion, A. / Poterszman, A. / Schultz, P. / Papai, G. / Ben-Shem, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qri.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qri.ent.gz | 963.9 KB | Display | PDB format |
PDBx/mmJSON format | 8qri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qri_validation.pdf.gz | 881.4 KB | Display | wwPDB validaton report |
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Full document | 8qri_full_validation.pdf.gz | 914.3 KB | Display | |
Data in XML | 8qri_validation.xml.gz | 86.5 KB | Display | |
Data in CIF | 8qri_validation.cif.gz | 131.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/8qri ftp://data.pdbj.org/pub/pdb/validation_reports/qr/8qri | HTTPS FTP |
-Related structure data
Related structure data | 18619MC 8qr1C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 438139.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q9Y4A5 |
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#2: Protein | Mass: 343867.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 References: UniProt: Q96L91, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human Tip60 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181210 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |