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Yorodumi- EMDB-12174: The catalytic core lobe of human telomerase in complex with a tel... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12174 | |||||||||
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Title | The catalytic core lobe of human telomerase in complex with a telomeric DNA substrate | |||||||||
Map data | Post-processed map | |||||||||
Sample |
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Keywords | Reverse transcriptase / ribonucleoprotein / complex / DNA / RNA BINDING PROTEIN | |||||||||
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 / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / : / establishment of protein localization to telomere / telomerase activity / nuclear telomere cap complex / siRNA processing / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / telomerase RNA binding / DNA biosynthetic process / RNA-templated transcription / telomeric DNA binding / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / Telomere Extension By Telomerase / 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 / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / 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 / PML body / transcription coactivator binding / 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 / protein-folding chaperone binding / cellular response to hypoxia / negative regulation of neuron apoptotic process / chromosome, telomeric region / tRNA binding / nuclear speck / protein heterodimerization activity / 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) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Nguyen THD / Ghanim GE | |||||||||
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_12174.map.gz | 48.5 MB | EMDB map data format | |
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Header (meta data) | emd-12174-v30.xml emd-12174.xml | 26.6 KB 26.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12174_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_12174.png | 109.9 KB | ||
Filedesc metadata | emd-12174.cif.gz | 8 KB | ||
Others | emd_12174_half_map_1.map.gz emd_12174_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12174 | HTTPS FTP |
-Validation report
Summary document | emd_12174_validation.pdf.gz | 949.8 KB | Display | EMDB validaton report |
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Full document | emd_12174_full_validation.pdf.gz | 949.4 KB | Display | |
Data in XML | emd_12174_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_12174_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12174 | HTTPS FTP |
-Related structure data
Related structure data | 7bg9MC 7bgbC C: citing same article (ref.) M: atomic model generated by this map |
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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_12174.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: #2
File | emd_12174_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12174_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human telomerase catalytic core in complex with a telomeric DNA s...
Entire | Name: Human telomerase catalytic core in complex with a telomeric DNA substrate |
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Components |
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-Supramolecule #1: Human telomerase catalytic core in complex with a telomeric DNA s...
Supramolecule | Name: Human telomerase catalytic core in complex with a telomeric DNA substrate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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-Supramolecule #2: Telomerase reverse transcriptase
Supramolecule | Name: Telomerase reverse transcriptase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Histone
Supramolecule | Name: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: DNA
Supramolecule | Name: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Telomerase reverse transcriptase,Telomerase reverse transcriptase
Macromolecule | Name: Telomerase reverse transcriptase,Telomerase reverse transcriptase type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Kidney |
Molecular weight | Theoretical: 149.158578 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKTAALAQHD EAVDNKFNKE QQNAFYEILH LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNDAQAPK VDNKFNKEQQ NAFYEILHL PNLNEEQRNA FIQSLKDDPS QSANLLAEAK KLNGAQAPKV DANSAGKSTD YDIPTTASEN LYFQGHKLGT F QGPWSHPQ ...String: MKTAALAQHD EAVDNKFNKE QQNAFYEILH LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNDAQAPK VDNKFNKEQQ NAFYEILHL PNLNEEQRNA FIQSLKDDPS QSANLLAEAK KLNGAQAPKV DANSAGKSTD YDIPTTASEN LYFQGHKLGT F QGPWSHPQ FEKGSAGSAA GSGAGWSHPQ FEKSRPTTAS GTMPRAPRCR AVRSLLRSHY REVLPLATFV RRLGPQGWRL VQ RGDPAAF RALVAQCLVC VPWDARPPPA APSFRQVSCL KELVARVLQR LCERGAKNVL AFGFALLDGA RGGPPEAFTT SVR SYLPNT VTDALRGSGA WGLLLRRVGD DVLVHLLARC ALFVLVAPSC AYQVCGPPLY QLGAATQARP PPHASGPRRR LGCE RAWNH SVREAGVPLG LPAPGARRRG GSASRSLPLP KRPRRGAAPE PERTPVGQGS WAHPGRTRGP SDRGFCVVSP ARPAE EATS LEGALSGTRH SHPSVGRQHH AGPPSTSRPP RPWDTPCPPV YAETKHFLYS SGDKEQLRPS FLLSSLRPSL TGARRL VET IFLGSRPWMP GTPRRLPRLP QRYWQMRPLF LELLGNHAQC PYGVLLKTHC PLRAAVTPAA GVCAREKPQG SVAAPEE ED TDPRRLVQLL RQHSSPWQVY GFVRACLRRL VPPGLWGSRH NERRFLRNTK KFISLGKHAK LSLQELTWKM SVRDCAWL R RSPGVGCVPA AEHRLREEIL AKFLHWLMSV YVVELLRSFF YVTETTFQKN RLFFYRKSVW SKLQSIGIRQ HLKRVQLRE LSEAEVRQHR EARPALLTSR LRFIPKPDGL RPIVNMDYVV GARTFRREKR AERLTSRVKA LFSVLNYERA RRPGLLGASV LGLDDIHRA WRTFVLRVRA QDPPPELYFV KVDVTGAYDT IPQDRLTEVI ASIIKPQNTY CVRRYAVVQK AAHGHVRKAF K SHVSTLTD LQPYMRQFVA HLQETSPLRD AVVIEQSSSL NEASSGLFDV FLRFMCHHAV RIRGKSYVQC QGIPQGSILS TL LCSLCYG DMENKLFAGI RRDGLLLRLV DDFLLVTPHL THAKTFLRTL VRGVPEYGCV VNLRKTVVNF PVEDEALGGT AFV QMPAHG LFPWCGLLLD TRTLEVQSDY SSYARTSIRA SLTFNRGFKA GRNMRRKLFG VLRLKCHSLF LDLQVNSLQT VCTN IYKIL LLQAYRFHAC VLQLPFHQQV WKNPTFFLRV ISDTASLCYS ILKAKNAGMS LGAKGAAGPL PSEAVQWLCH QAFLL KLTR HRVTYVPLLG SLRTAQTQLS RKLPGTTLTA LEAAANPALP SDFKTILD UniProtKB: Telomerase reverse transcriptase |
-Macromolecule #3: Histone H2B
Macromolecule | Name: Histone H2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Kidney |
Molecular weight | Theoretical: 18.074932 KDa |
Sequence | String: MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSNPRN LSPTKPGGSE DRQPPPSQLS AIPPFCLVLR A GIAGQV UniProtKB: Histone H2B |
-Macromolecule #4: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Kidney |
Molecular weight | Theoretical: 14.140584 KDa |
Sequence | String: MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VRRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A |
-Macromolecule #2: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*AP*GP*GP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 5.514567 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DA)(DG)(DG)(DG) |
-Macromolecule #5: RNA (256-MER)
Macromolecule | Name: RNA (256-MER) / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Kidney |
Molecular weight | Theoretical: 145.477797 KDa |
Sequence | String: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ...String: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ACAAAAAAUG UCAGCUGCUG GCCCGUUCGC CCCUCCCGGG GACCUGCGGC GGGUCGCCUG CCCAGCCCCC GA ACCCCGC CUGGAGGCCG CGGUCGGCCC GGGGCUUCUC CGGAGGCACC CACUGCCACC GCGAAGAGUU GGGCUCUGUC AGC CGCGGG UCUCUCGGGG GCGAGGGCGA GGUUCAGGCC UUUCAGGCCG CAGGAAGAGG AACGGAGCGA GUCCCCGCGC GCGG CGCGA UUCCCUGAGC UGUGGGACGU GCACCCAGGA CUCGGCUCAC ACAUGC |
-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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4-5 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 80 |
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Output model | PDB-7bg9: |