- EMDB-14737: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-14737
Title
Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
Map data
Sample
Complex: Complex of human INO80core bound to a WT nucleosome
Protein or peptide: x 10 types
DNA: x 2 types
Ligand: x 3 types
Keywords
chromatin remodeler / transcription / replication / DNA repair / DNA BINDING PROTEIN
Function / homology
Function and homology information
positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body ...positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / UV-damage excision repair / protein folding chaperone complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / mitotic sister chromatid segregation / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / negative regulation of tumor necrosis factor-mediated signaling pathway / alpha-tubulin binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / spindle assembly / ATP-dependent activity, acting on DNA / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / regulation of DNA repair / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / TBP-class protein binding / telomere organization / DNA helicase activity / positive regulation of DNA repair / telomere maintenance / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to estradiol stimulus / HDACs deacetylate histones / cellular response to ionizing radiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of canonical Wnt signaling pathway / euchromatin / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / Metalloprotease DUBs / PKMTs methylate histone lysines / ADP binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / nuclear matrix / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin Similarity search - Function
Name: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8.
-
Electron microscopy
Microscope
TFS KRIOS
Temperature
Min: 77.15 K / Max: 77.15 K
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 9760 / Average exposure time: 5.1 sec. / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi