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Yorodumi- EMDB-12175: Low resolution reconstruction of whole human telomerase class 2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12175 | |||||||||
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Title | Low resolution reconstruction of whole human telomerase class 2 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / telomerase RNA localization to Cajal body / protein localization to Cajal body / Cajal body organization / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / positive regulation of hair cycle ...telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / telomerase RNA localization to Cajal body / protein localization to Cajal body / Cajal body organization / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / rRNA pseudouridine synthesis / RNA-directed RNA polymerase complex / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / siRNA transcription / telomerase RNA stabilization / positive regulation of protein localization to nucleolus / enzyme-directed rRNA pseudouridine synthesis / box H/ACA snoRNA binding / regulation of telomerase RNA localization to Cajal body / mRNA pseudouridine synthesis / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / : / pseudouridine synthase activity / establishment of protein localization to telomere / telomerase activity / scaRNA localization to Cajal body / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / nuclear telomere cap complex / siRNA processing / sno(s)RNA-containing ribonucleoprotein complex / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / telomerase RNA binding / rRNA modification in the nucleus and cytosol / positive regulation of double-strand break repair / DNA biosynthetic process / RNA-templated transcription / telomeric DNA binding / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of stem cell proliferation / mitochondrial nucleoid / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of cellular senescence / Telomere Extension By Telomerase / RNA folding / positive regulation of double-strand break repair via homologous recombination / telomere maintenance via telomerase / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / replicative senescence / positive regulation of Wnt signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / RNA processing / negative regulation of endothelial cell apoptotic process / response to cadmium ion / Cajal body / : / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of telomere maintenance via telomerase / positive regulation of DNA repair / telomere maintenance / mitochondrion organization / maturation of LSU-rRNA / positive regulation of nitric-oxide synthase activity / positive regulation of glucose import / Formation of the beta-catenin:TCF transactivating complex / regulation of protein stability / PML body / fibrillar center / transcription coactivator binding / positive regulation of miRNA transcription / RNA-directed DNA polymerase / rRNA processing / structural constituent of chromatin / positive regulation of angiogenesis / RNA-directed DNA polymerase activity / nucleosome / positive regulation of protein binding / site of double-strand break / histone binding / protein-folding chaperone binding / cellular response to hypoxia / negative regulation of neuron apoptotic process / cytosolic large ribosomal subunit / chromosome, telomeric region / tRNA binding / nuclear body / nuclear speck / protein heterodimerization activity / negative regulation of gene expression / RNA-dependent RNA polymerase activity / DNA repair Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Nguyen THD / Ghanim GE / Fountain AJ / van Roon AMM / Rangan R / Das R / Collins K | |||||||||
Funding support | United Kingdom, United States, 2 items
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Citation | Journal: Nature / Year: 2021 Title: Structure of human telomerase holoenzyme with bound telomeric DNA. Authors: George E Ghanim / Adam J Fountain / Anne-Marie M van Roon / Ramya Rangan / Rhiju Das / Kathleen Collins / Thi Hoang Duong Nguyen / Abstract: Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis ...Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis and in cancers, and mutations that compromise the function of telomerase result in disease. A previous structure of human telomerase at a resolution of 8 Å revealed a vertebrate-specific composition and architecture, comprising a catalytic core that is flexibly tethered to an H and ACA (hereafter, H/ACA) box ribonucleoprotein (RNP) lobe by telomerase RNA. High-resolution structural information is necessary to develop treatments that can effectively modulate telomerase activity as a therapeutic approach against cancers and disease. Here we used cryo-electron microscopy to determine the structure of human telomerase holoenzyme bound to telomeric DNA at sub-4 Å resolution, which reveals crucial DNA- and RNA-binding interfaces in the active site of telomerase as well as the locations of mutations that alter telomerase activity. We identified a histone H2A-H2B dimer within the holoenzyme that was bound to an essential telomerase RNA motif, which suggests a role for histones in the folding and function of telomerase RNA. Furthermore, this structure of a eukaryotic H/ACA RNP reveals the molecular recognition of conserved RNA and protein motifs, as well as interactions that are crucial for understanding the molecular pathology of many mutations that cause disease. Our findings provide the structural details of the assembly and active site of human telomerase, which paves the way for the development of therapeutic agents that target this enzyme. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12175.map.gz | 225.4 MB | EMDB map data format | |
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Header (meta data) | emd-12175-v30.xml emd-12175.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12175_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_12175.png | 32.9 KB | ||
Others | emd_12175_half_map_1.map.gz emd_12175_half_map_2.map.gz | 194.2 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12175 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12175 | HTTPS FTP |
-Validation report
Summary document | emd_12175_validation.pdf.gz | 339.3 KB | Display | EMDB validaton report |
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Full document | emd_12175_full_validation.pdf.gz | 338.4 KB | Display | |
Data in XML | emd_12175_validation.xml.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12175 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12175 | HTTPS FTP |
-Related structure data
Related structure data | 7bg9C 7bgbC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10732 (Title: Structure of human telomerase holoenzyme with bound telomeric DNA Data size: 11.2 TB Data #1: Unaligned multiframe micrographs of human telomerase holoenzyme bound to a telomeric DNA [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12175.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_12175_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12175_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Whole human telomerase reconstruction class 2
Entire | Name: Whole human telomerase reconstruction class 2 |
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Components |
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-Supramolecule #1: Whole human telomerase reconstruction class 2
Supramolecule | Name: Whole human telomerase reconstruction class 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 Details: Low resolution reconstruction of human telomerase containing both catalytic core and H/ACA lobe linked by flexible RNA linkers. |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293T / Recombinant plasmid: pcDNA3.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.0 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: 43639 / Average exposure time: 1.0 sec. / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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