+Open data
-Basic information
Entry | Database: PDB / ID: 8xvt | ||||||
---|---|---|---|---|---|---|---|
Title | The core subcomplex of human NuA4/TIP60 complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / Remodeler / Histone Acetyltransferase Complex / NuA4 / TIP60 | ||||||
Function / homology | Function and homology information 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 / brahma complex / R2TP 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 / positive regulation of T cell differentiation / apical junction complex / 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 / maintenance of blood-brain barrier / cortical cytoskeleton / 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 / RHO GTPases activate IQGAPs / RNA polymerase II core promoter sequence-specific DNA binding / 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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Chen, K. / Wang, L. / Yu, Z. / Yu, J. / Ren, Y. / Wang, Q. / Xu, Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xvt.cif.gz | 943.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xvt.ent.gz | 734.4 KB | Display | PDB format |
PDBx/mmJSON format | 8xvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/8xvt ftp://data.pdbj.org/pub/pdb/validation_reports/xv/8xvt | HTTPS FTP |
---|
-Related structure data
Related structure data | 38718MC 8xvgC 8xvvC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 6 types, 11 molecules ACEBDFGIJKN
#1: Protein | Mass: 50296.914 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y265, DNA helicase #2: Protein | Mass: 51222.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y230, DNA helicase #3: Protein | | Mass: 53090.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DMAP1, KIAA1425 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9NPF5 #5: Protein | Mass: 47509.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: O96019 #6: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): Expi293F / Production host: Homo sapiens (human) References: UniProt: P60709, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #8: Protein | | Mass: 40658.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS72, TCFL1, YL1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q15906 |
---|
-Isoform 2 of ... , 2 types, 2 molecules HM
#4: 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 |
---|---|
#7: Protein | Mass: 90988.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPC1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9H2F5 |
-Non-polymers , 1 types, 9 molecules
#9: Chemical | ChemComp-ADP / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The core subcomplex of human NuA4/TIP60 complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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: 2800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 701594 / Symmetry type: POINT |
Atomic model building | PDB-ID: 6IGM Accession code: 6IGM / Source name: PDB / Type: experimental model |