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Yorodumi- EMDB-2311: Three-dimensional structure of active, full-length human telomera... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2311 | |||||||||
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Title | Three-dimensional structure of active, full-length human telomerase. Independently refined open monomer structure, determined by single-particle electron microscopy in negative stain | |||||||||
Map data | Three-dimensional structure of active, full-length human telomerase. Independently refined open monomer structure, determined by single-particle electron microscopy in negative stain | |||||||||
Sample |
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Keywords | Telomerase reverse transcriptase / human / telomere length extension | |||||||||
Function / homology | Function and homology information positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / telomerase activity ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / : / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / nuclear telomere cap complex / siRNA processing / Telomere Extension By Telomerase / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / positive regulation of G1/S transition of mitotic cell cycle / telomeric DNA binding / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / telomere maintenance via telomerase / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of Wnt signaling pathway / replicative senescence / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of miRNA transcription / mitochondrion organization / 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 / transcription coactivator binding / RNA-directed DNA polymerase / positive regulation of angiogenesis / RNA-directed DNA polymerase activity / positive regulation of protein binding / cellular response to hypoxia / protein-folding chaperone binding / chromosome, telomeric region / negative regulation of neuron apoptotic process / tRNA binding / nuclear speck / negative regulation of gene expression / RNA-dependent RNA polymerase activity / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Sauerwald A / Sandin S / Cristofari G / Scheres SHW / Lingner J / Rhodes D | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2013 Title: Structure of active dimeric human telomerase. Authors: Anselm Sauerwald / Sara Sandin / Gaël Cristofari / Sjors H W Scheres / Joachim Lingner / Daniela Rhodes / Abstract: Telomerase contains a large RNA subunit, TER, and a protein catalytic subunit, TERT. Whether telomerase functions as a monomer or dimer has been a matter of debate. Here we report biochemical and ...Telomerase contains a large RNA subunit, TER, and a protein catalytic subunit, TERT. Whether telomerase functions as a monomer or dimer has been a matter of debate. Here we report biochemical and labeling data that show that in vivo-assembled human telomerase contains two TERT subunits and binds two telomeric DNA substrates. Notably, catalytic activity requires both TERT active sites to be functional, which demonstrates that human telomerase functions as a dimer. We also present the three-dimensional structure of the active full-length human telomerase dimer, determined by single-particle EM in negative stain. Telomerase has a bilobal architecture with the two monomers linked by a flexible interface. The monomer reconstruction at 23-Å resolution and fitting of the atomic structure of the TERT subunit from beetle Tribolium castaneum into the EM density reveals the spatial relationship between RNA and protein subunits, providing insights into telomerase architecture. | |||||||||
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_2311.map.gz | 50 KB | EMDB map data format | |
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Header (meta data) | emd-2311-v30.xml emd-2311.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | EMD-2311.png | 46.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2311 | HTTPS FTP |
-Validation report
Summary document | emd_2311_validation.pdf.gz | 218 KB | Display | EMDB validaton report |
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Full document | emd_2311_full_validation.pdf.gz | 217.1 KB | Display | |
Data in XML | emd_2311_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2311 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2311 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2311.map.gz / Format: CCP4 / Size: 53.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Three-dimensional structure of active, full-length human telomerase. Independently refined open monomer structure, determined by single-particle electron microscopy in negative stain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Three-dimensional structure of active, full-length human telomera...
Entire | Name: Three-dimensional structure of active, full-length human telomerase dimer, determined by single-particle electron microscopy in negative stain |
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Components |
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-Supramolecule #1000: Three-dimensional structure of active, full-length human telomera...
Supramolecule | Name: Three-dimensional structure of active, full-length human telomerase dimer, determined by single-particle electron microscopy in negative stain type: sample / ID: 1000 Details: Independently refined open monomer structure. The composition analysed by mass spectroscopy.Purified telomerase contains the hTERT subunits and two accessory proteins, Nop10 and dyskerin. ...Details: Independently refined open monomer structure. The composition analysed by mass spectroscopy.Purified telomerase contains the hTERT subunits and two accessory proteins, Nop10 and dyskerin. Telomerase complexes have a molecular weight consistent with that of a dimer consisting of two hTERT (127 kDa) and two hTER (153 kDa) subunits, as well as the two accessory proteins Nop10 (7.7 kDa) and dyskerin (58 kDA). Number unique components: 1 |
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Molecular weight | Method: Sedimentation |
-Macromolecule #1: Telomerase reverse transcriptase
Macromolecule | Name: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 1 / Name.synonym: TERT / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: Human Embryonic Kidney cells |
Molecular weight | Experimental: 127 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK239T / Recombinant plasmid: pCDNA6 |
Sequence | UniProtKB: Telomerase reverse transcriptase / GO: telomere maintenance / InterPro: Telomerase reverse transcriptase |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM Tris, 150 mM KCl, 1 mM MgCl2 |
Staining | Type: NEGATIVE Details: Continuous carbon-coated grids were freshly prepared and glow-discharged before use. 13 microl of telomerase sample (8-10 nM) were deposited on the grid for 15-30 minutes, blotted with ...Details: Continuous carbon-coated grids were freshly prepared and glow-discharged before use. 13 microl of telomerase sample (8-10 nM) were deposited on the grid for 15-30 minutes, blotted with filter paper and negatively stained with 2 drops of 1-2% (w/v) uranyl acetate solution. |
Grid | Details: 200 mesh carbon coated with thin carbon, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Alignment procedure | Legacy - Astigmatism: Corrected at 100,000 times magnification |
Details | The films were developed in Kodak developer at full strength for 12 min. |
Date | Jan 1, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 482 / Average electron dose: 10 e/Å2 / Details: The micrographs were compressed x4 / Od range: 1.4 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 42550 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0015 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Details | 4690 sub-images were selected of the open monomer from 2D class averages of telomerase dimer side-views, used for independent monomer refinement. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: EMAN2, XMIPP / Number images used: 4690 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |