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Yorodumi- PDB-7qxb: Cryo-EM map of human telomerase-DNA-TPP1-POT1 complex (sharpened map) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qxb | |||||||||
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Title | Cryo-EM map of human telomerase-DNA-TPP1-POT1 complex (sharpened map) | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN / Reverse transcriptase / ribonucleoprotein / telomerase / telomere / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of DNA strand elongation / regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / 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 DNA strand elongation / regulation of DNA helicase activity / G-rich single-stranded DNA binding / telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / telomerase catalytic core complex / siRNA transcription / positive regulation of protein localization to nucleolus / regulation of double-strand break repair via nonhomologous end joining / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / telomerase activity / positive regulation of helicase activity / telomerase inhibitor activity / telomerase RNA reverse transcriptase activity / DEAD/H-box RNA helicase binding / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / positive regulation of DNA helicase activity / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / negative regulation of telomerase activity / nuclear telomere cap complex / siRNA processing / single-stranded telomeric DNA binding / positive regulation of telomere maintenance / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomerase RNA binding / telomere capping / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / DNA duplex unwinding / telomeric DNA binding / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / positive regulation of Wnt signaling pathway / telomere maintenance via telomerase / replicative senescence / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / response to cadmium ion / negative regulation of endothelial cell apoptotic process / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of telomerase activity / positive regulation of vascular associated smooth muscle cell proliferation / 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 / positive regulation of telomere maintenance via telomerase / telomere maintenance / 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 / transcription coactivator binding / DNA Damage/Telomere Stress Induced Senescence / PML body / positive regulation of miRNA transcription / RNA-directed DNA polymerase / structural constituent of chromatin / positive regulation of angiogenesis / RNA-directed DNA polymerase activity / nucleosome / positive regulation of protein binding / cellular response to hypoxia / protein-folding chaperone binding / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / nuclear body / nuclear speck / protein heterodimerization activity / RNA-dependent RNA polymerase activity / negative regulation of gene expression / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Sekne, Z. / Ghanim, G.E. / van Roon, A.M.M. / Nguyen, T.H.D. | |||||||||
Funding support | United Kingdom, United States, 2items
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Citation | Journal: Science / Year: 2022 Title: Structural basis of human telomerase recruitment by TPP1-POT1. Authors: Zala Sekne / George E Ghanim / Anne-Marie M van Roon / Thi Hoang Duong Nguyen / Abstract: Telomerase maintains genome stability by extending the 3' telomeric repeats at eukaryotic chromosome ends, thereby counterbalancing progressive loss caused by incomplete genome replication. In ...Telomerase maintains genome stability by extending the 3' telomeric repeats at eukaryotic chromosome ends, thereby counterbalancing progressive loss caused by incomplete genome replication. In mammals, telomerase recruitment to telomeres is mediated by TPP1, which assembles as a heterodimer with POT1. We report structures of DNA-bound telomerase in complex with TPP1 and with TPP1-POT1 at 3.2- and 3.9-angstrom resolution, respectively. Our structures define interactions between telomerase and TPP1-POT1 that are crucial for telomerase recruitment to telomeres. The presence of TPP1-POT1 stabilizes the DNA, revealing an unexpected path by which DNA exits the telomerase active site and a DNA anchor site on telomerase that is important for telomerase processivity. Our findings rationalize extensive prior genetic and biochemical findings and provide a framework for future mechanistic work on telomerase regulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7qxb.cif.gz | 471.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qxb.ent.gz | 363.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qxb ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qxb | HTTPS FTP |
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-Related structure data
Related structure data | 14197MC 7qxaC 7qxsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules ALMOP
#1: Protein | Mass: 127195.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERT, EST2, TCS1, TRT / Plasmid: pcDNA3.1 / Details (production host): pcDNA3.1-ZZSS-TERT / Cell (production host): epithelial / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O14746, RNA-directed DNA polymerase |
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#3: Protein | Mass: 14140.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Organ: Kidney / Tissue: Kidney / References: UniProt: B2R5B3 |
#4: Protein | Mass: 18074.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Organ: Kidney / Tissue: Kidney / References: UniProt: B4DR52 |
#6: Protein | Mass: 49013.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, hCG_27140 / Plasmid: p-FASTBac Dual / Cell (production host): epithelial / Organ (production host): ovary / Production host: Spodoptera (butterflies/moths) / Tissue (production host): ovary / References: UniProt: A0A590TQL1 |
#7: Protein | Mass: 71520.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Plasmid: p-FASTBac Dual / Cell (production host): epithelial / Organ (production host): ovary / Production host: Spodoptera (butterflies/moths) / Tissue (production host): ovary / References: UniProt: Q9NUX5 |
-RNA chain / DNA chain , 2 types, 2 molecules BN
#2: RNA chain | Mass: 145477.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Details (production host): pcDNA3.1 U3-hTR-HDV / Cell (production host): epithelial / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: GenBank: NR_001566 |
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#5: DNA chain | Mass: 9501.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Calibrated magnification: 45871 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 50775 Details: Images were collected in movie-mode and fractionated into 48 movie frames |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: REFMAC / Version: 5.8.0256 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 21589656 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192871 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7BG9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.91→164.59 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 119.536 / SU ML: 1.312 / ESU R: 0.905 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 220.612 Å2
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Refinement step | Cycle: 1 / Total: 17193 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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