Secondary structures
Currently there are 56 species, 33 vertebrates, 1 fungus, and 22 ciliates, for which the secondary structures of the RNA component of telomerase (TR) have been determined. These structures were constructed from the alignment of TR sequences and secondary structure prediction. Presented within the secondary structure is the primary sequence, baseparing confirmed by covariation, labeled template and pseudoknot, conserved regions, and the various domains. Where applicable, a reference citation to the original article that is linked to the online journal. The structures are organized by taxonomy. The view button will open a separate browser window with a .jpg of the secondary structure requested. Renderings of the secondary structures are available for download in high quality .pdf as well as .jpg formats.
Component | Species | Structures | References | |||
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TR | Vertebrates | Homo sapiens (human) | View | .jpg | Chen et al, 2000 | |
Tupaia glis belangeri (common tree shrew) | View | .jpg | Chen et al, 2000 | |||
Oryctolagus cuniculus (domestic rabbit) | View | .jpg | Chen et al, 2000 | |||
Cavia porcellus (domestic guinea pig) | View | .jpg | Chen et al, 2000 | |||
Chinchilla brevicaudata (short-tailed chinchilla) | View | .jpg | Chen et al, 2000 | |||
Geomys breviceps (gopher) | View | .jpg | Chen et al, 2000 | |||
Microtus ochrogaster (prairie vole) | View | .jpg | Chen et al, 2000 | |||
Cricetulus griseus (Chinese hamster) | View | .jpg | Chen et al, 2000 | |||
Mus musculus (mouse) | View | .jpg | Chen et al, 2000 | |||
Rattus norvegicus (Norway rat) | View | .jpg | Chen et al, 2000 | |||
Mustela putorius furo (domestic ferret) | View | .jpg | Chen et al, 2000 | |||
Procyon lotor (raccoon) | View | .jpg | Chen et al, 2000 | |||
Bos taurus (cattle) | View | .jpg | Chen et al, 2000 | |||
Sus scrofa (pig) | View | .jpg | Chen et al, 2000 | |||
Suncus murinus (Asian house shrew) | View | .jpg | Chen et al, 2000 | |||
Equus caballus (domestic horse) | View | .jpg | Chen et al, 2000 | |||
Dasypus novemcinctus (armadillo) | View | .jpg | Chen et al, 2000 | |||
Dasyurus hallucatus (northern quoll) | View | .jpg | Chen et al, 2000 | |||
Elephas maximus (Asian elephant) | View | .jpg | Chen et al, 2000 | |||
Trichechus manatus (Caribbean manatee) | View | .jpg | Chen et al, 2000 | |||
Anodorhynchus hyacinthinus (macaw) | View | .jpg | Chen et al, 2000 | |||
Gallus gallus (chicken) | View | .jpg | Chen et al, 2000 | |||
Chelydra serpentina (snapping turtle) | View | .jpg | Chen et al, 2000 | |||
Bombina japonica (toad) | View | .jpg | Chen et al, 2000 | |||
Xenopus laevis (African clawed frog) | View | .jpg | Chen et al, 2000 | |||
Ceratophrys ornata (ornate horned frog) | View | .jpg | Chen et al, 2000 | |||
Pyxicephalus adspersus (bull frog) | View | .jpg | Chen et al, 2000 | |||
Dermophis mexicanus (Mexican caecilian) | View | .jpg | Chen et al, 2000 | |||
Herpele squalostoma (Congo caecilians) | View | .jpg | Chen et al, 2000 | |||
Typhlonectes natans (Rio Cauca caecilian) | View | .jpg | Chen et al, 2000 | |||
Oryzias latipes (Medaka) | View | .jpg | Xie et al, 2007 | |||
Gasterosteus aculeatus (stickleback) | View | .jpg | Xie et al, 2007 | |||
Takifugu rubripes (Fugu fish) | View | .jpg | Xie et al, 2007 | |||
Tetraodon nigroviridis (green puffer fish) | View | .jpg | Xie et al, 2007 | |||
Danio rerio (zebrafish) | View | .jpg | Xie et al, 2007 | |||
Rhizoprionodon porosus (sharpnose shark) | View | .jpg | Chen et al, 2000 | |||
Mustelus canis (smooth dogfish shark) | Chen et al, 2000 | |||||
Dasyatis sabina (Atlantic stingray) | View | .jpg | Chen et al, 2000 | |||
Rhinoptera bonasus (cownose ray) | View | .jpg | Chen et al, 2000 | |||
Fungi | Ustilago maydis (corn smut fungus) | View | .jpg | Logeswaran et al, 2022 | ||
Saccharomyces cerevisiae (baker's yeast) | View | .jpg | ||||
Saccharomyces castellii | View | .jpg | Brown et al, 2007 Dandjinou et al, 2004 Chappell and Lundblad, 2004 |
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Kluyveromyces lactis | View | .jpg | Brown et al, 2007 Chappell and Lundblad, 2004 |
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Ciliates | Tetrahymena thermophila | View | .jpg | |||
Tetrahymena malaccensis | View | .jpg | ||||
Tetrahymena pyriformis | View | .jpg | ||||
Tetrahymena vorax | View | .jpg | ||||
Tetrahymena borealis | View | .jpg | McCormick-Graham et al, 1995 | |||
Tetrahymena silvana | View | .jpg | ||||
Tetrahymena australis | View | .jpg | ||||
Tetrahymena pigmentosa | View | .jpg | ||||
Tetrahymena hyperangularis | View | .jpg | ||||
Tetrahymena capricornis | View | .jpg | McCormick-Graham et al, 1995 | |||
Tetrahymena hegewischi | View | .jpg | ||||
Tetrahymena paravorax | View | .jpg | McCormick-Graham et al, 1995 | |||
Paramecium tetraurelia | View | .jpg | McCormick-Graham et al, 1996 | |||
Paramecium primaurelia | View | .jpg | ||||
Paramecium multimicronucleatum | View | .jpg | McCormick-Graham et al, 1996 | |||
Euplotes aediculatus | View | .jpg | Lingner et al, 1994 | |||
Euplotes eurystomus | View | .jpg | Lingner et al, 1994 | |||
Euplotes crassus | View | .jpg | Lingner et al, 1994 | |||
Oxytricha nova (Sterkiella nova) | View | .jpg | Lingner et al, 1994 | |||
Oxytricha trifallax (Sterkiella histriomuscorum) | View | .jpg | Lingner et al, 1994 | |||
Stylonychia mytilis | View | .jpg | Lingner et al, 1994 | |||
Stylonychia lemnae | View | .jpg | Lingner et al, 1994 |
Tertiary structures
The following table is a listing of various tertiary structure fragments from the telomerase ribonucleoprotein. The tertiary RNA structures were derived from NMR spectroscopy while the tertiary protein structures were derived from X-ray crystallography and NMR spectroscopy. Below is a brief discription of the protein or fragment, the protein data bank (PDB) ID number linked to Research Collaboratory for Structural Bioinformatics (RCSB) record, and the reference to the original article linked to the online journal. The structures are organized by component and taxonomy. The tertiary structures can be viewed online within the browser, or can be downloaded from the .pdb link and viewed by a separate molecular visualization program. A standard nomenclature is used throughout the online database for consistency and clarity. Homologous proteins are given a single name for simplicity.
The view button will open a separate browser window for the .pdb of the tertiary structure requested. To view the structures within the browser, java is required and is available from Sun Microsystems. The tertiary structures presented within the separate browser window can be set to various renderings. The proteins and nucleic acids are depicted by specific colors. The tertiary structures are available for download in .pdb file format. A molecular visualization program, such as PyMol, RasMol, or Swiss-PdbViwer, is necessary for rendering. The direct links for the download pages are available for Pymol, RasMol, and Swiss-PdbViewer. The image on the home page to the database was constructed from the .pdb files listed and rendered in Pymol.
Component | Species | Structure | PDB ID | References | ||
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TR | Homo sapiens (human) | p2b hairpin | 1NA2 | Theimer et al, 2003 | ||
P2b, P3 pseudoknot | 1YMO | Theimer et al, 2005 | ||||
P2b hairpin (dyskeratosis congenita mutant) | 1Q75 | Theimer et al, 2005 | ||||
P6 hairpin | 1Z31 | Leeper et al, 2005 | ||||
P6.1 stem loop | 1OQ0 | Leeper et al, 2003 | ||||
P8b hairpin | 2QH2 | Theimer et al, 2007 | ||||
Oryzias latipes (Medaka) | CR4/5 | 2MHI | Kim et al, 2014 | |||
Tetrahymena thermophila | stem loop IV | 2FEY | Chen et al, 2006 | |||
stem loop IV | 2H2X | Richards et al, 2006a | ||||
helix II template boundary element | 2FRL | Richards et al, 2006b | ||||
TERT | Oryzias latipes (Medaka) | RNA binding domain with CR4/5 | 4O26 | Huang et al, 2014 | ||
Takifugu rubripes (Fugu fish) | RNA binding domain | 4LMO | Harkisheimer et al, 2013 | |||
Tribolium castaneum | catalytic subunit | 3DU6 | Gillis et al, 2008 | |||
catalytic subunit with DNA-RNA stem-loop | 3KYL | Mitchell et al, 2010 | ||||
novel telomerase inhibitor | 6E53 | Hernandez-Sanchez et al, 2019 | ||||
reverse transcriptase product complex | 6USP | Schaich et al, 2020 | ||||
Tetrahymena thermophila | TEN domain | 2B2A | Jacobs et al, 2006 | |||
RNA binding domain | 2R4G | Rouda et al, 2007 | ||||
Telomerase Complex | Tetrahymena thermophila | Holoenzyme | 6D6V | Jiansen et al, 2018 | ||
Homo Sapiens | Holoenzyme | EMD7518 | Thi et al, 2018 | |||
Holoenzyme | 7BG9 | Ghanim et al, 2021 | ||||
Holoenzyme | 7BGB | Ghanim et al, 2021 | ||||
Tetrahymena thermophila | Holoenzyme | 7LMB | He et al, 2021 | |||
Holoenzyme | 7LMA | He et al, 2021 | ||||
Telomerase-associated Proteins | H/ACA ribonucleoprotein complex (dyskerin, Nop10, Gar1, NHP2) | |||||
Pyrococcus furiosus | Cbf5, Nop10, Gar1, L7Ae, H/ACA RNA complex | 2HVY | Li et al, 2006 | |||
Cbf5, Nop10, Gar1 complex | 2EY4 | Rashid et al, 2006 | ||||
Pyrococcus abyssi | Cbf5, Nop10 complex | 2AUS | Manival et al, 2006 | |||
Methanococcus jannaschii | Cbf5, Nop10 complex | 2APO | Hamma et al., 2005 | |||
associated proteins | ||||||
Homo sapiens (human) | Est1A (Pin domain) | 2DOK | Tanokura et al, 2007 | |||
Est1A (Pin domain) | 2HWW | Glavan et al, 2006 | ||||
Est1A (Pin domain, E1282C mutant) | 2HWX | Glavan et al, 2006 | ||||
Est1B (Pinc domain) | 2HWY | Glavan et al, 2006 | ||||
Tetrahymena thermophila | P45 C-terminal domain | 5DFN | Jiang et al, 2015 | |||
p19 fused to MBP | 5DFM | Jiang et al, 2015 | ||||
P65 C-terminal domain solution structure | 2LSL | Singh et al, 2012 | ||||
P65 C-terminal domain with stem IV | 4ERD | Singh et al, 2012 | ||||
P65 C-terminal domain crystal structure | 4EYT | Singh et al, 2012 | ||||
chaperones | ||||||
Homo sapiens (human) | hsp70 (N-terminal ATPase domain) | 1HJO | Osipiuk et al, 1999 | |||
hsp70, hop (TPR1 domain) complex | 1ELW | Morshauser et al, 2000 | ||||
hsp90, hop (TPR2A domain) complex | 1ELR | Scheufler et al, 2000 | ||||
hsp90 | 1OSF | Jez et al, 2003 | ||||
Bos taurus (cattle) | hsc70 | 1ATR | O'Brien et al, 1993 | |||
Rattus norvegicus (Norway rat) | hsc70 (substrate binding domain) | 1CKR | Zuiderweg et al, 1999 | |||
Saccharomyces cerevisiae (yeast) | hsp40, hsp70 complex (C-terminal domains) | 2B26 | Li et al, 2006 | |||
hsp90, ATP complex | 1AM1 | Prodromou et al, 1997 | ||||
hsp90, ADP copmlex | 1AMW | Prodromou et al, 1997 | ||||
Escherichia coli | DnaK (substrate binding domain) | 1BPR | Wang et al, 1998 | |||
DnaK (substrate binding domain) | 1DKZ | Zhu et al, 1999 | ||||
Telomere-associated Proteins | sherlterin complex - primary telomeric DNA-binding proteins (Pot1, TRF1, and TRF2) | |||||
protection of telomere 1 (Pot1) | ||||||
Homo sapiens (human) | Pot1, ssDNA complex | 1XJV | Lei et al, 2004 | |||
Schizosaccharomyces pombe | Pot1, ssDNA complex | 1QZH | Lei et al, 2003 | |||
telomeric repeat binding factors 1 and 2 (TRF1 and TRF2) | ||||||
Homo sapiens (human) | TRF1 (DNA binding domain), dsDNA complex | 1IV6 | Nishikawa et al, 2001 | |||
TRF1 (DNA binding domain), dsDNA complex | 1W0T | Rhodes et al, 2005 | ||||
TRF1 (DNA binding domain) | 1BA5 | Nishikawa et al, 1998 | ||||
TRF1 (dimerization domain) | 1H6O | Fairall et al, 2001 | ||||
TRF1 (TRF domain), TIN2 (NL signal) complex | 3BQO | Chen et al, 2008 | ||||
TRF2 (dimerization domain) | 1H6P | Fairall et al, 2001 | ||||
TRF2 (DNA binding domain), dsDNA complex | 1VFC | Hanaoka et al, 2005 | ||||
TRF2 (DNA binding domain), dsDNA complex | 1W0U | Rhodes et al, 2005 | ||||
TRF2 (DNA binding domain) | 1VF9 | Hanaoka et al, 2005 | ||||
TRF2 (C-terminal Myb domain) | 1XG1 |
(direct link)
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Nicotiana tabacum | TRF1 (DNA binding domain) | 2CKX |
Cho et al, 2007
(to be published)
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Arabidopsis thaliana | TRP (DNA binding domain, like TRF) | 2AJE | Sue et al, 2006 | |||
sherlterin complex - proteins associate with the telomeric DNA-binding proteins (TIN2, TPP1, and Rap1) | ||||||
TRF1-interacting nuclear factor 2 (TIN2) | ||||||
adrenocortical dysplasia homolog (TPP1) | ||||||
Homo sapiens (human) | TPP1 | 2I46 | Wang et al, 2007 | |||
TRF2-interacting protein (Rap1) | ||||||
Homo sapiens (human) | RAP1 (MYB domain) | 1FEX | Hanaoka et al, 2001 | |||
Saccharomyces cerevisiae (yeast) | RAP1 (DNA-binding domain), dsDNA complex | 1IGN | Konig et al, 1996 | |||
telomere binding protein (TBP) | ||||||
Oxytricha nova (Sterkiella nova) | TBP, ssDNA complex | 1OTC | Horvath et al, 1998 | |||
TBP, ssDNA complex | 2I0Q | Buczek et al, 2006 | ||||
TBP, ssDNA complexed and uncomplexed | 1K8G | Classen et al, 2001 | ||||
TBP, ssDNA, DNA quadruplex complex | 1JB7 | Horvath et al, 2001 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PA6 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH2 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH3 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH4 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH5 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH6 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH7 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH8 | Theobald et al, 2003 | ||||
TBP, ssDNA, DNA quadruplex complex | 1PH9 | Theobald et al, 2003 | ||||
TBP (alpha subunit), ssDNA complex | 1KIX | Peersen et al, 2002 | ||||
telomere-associated proteins | ||||||
Saccharomyces cerevisiae (yeast) | Cdc13 (DNA binding domain) | 1KXL | Mitton-Fry et al, 2002 | |||
Bombyx mori (domestic silkworm) | TRAS1 (N-terminal domain) | 1WDU | Maita et al, 2004 | |||
Homo sapiens (humans) | HOT1 | 4J19 | Kappei et al, 2013 | |||
Telomeric DNA | Homo sapiens (human) | quadruplex (AGGG[TTAGGG]3) | 143D | Wang et al, 1993 | ||
tetrad (AGGGT) | 1EVM | Patel et al, 1999 | ||||
quadruplex (TAGGGT)2 | 1K8P | Parkinson et al, 2002 | ||||
parallel-stranded quadruplex (TTAGGGT) | 1NZM | Gavathiotis et al, 2003 | ||||
parallel-stranded quadruplex (TTAGGGT) | 1NP9 | Gavathiotis et al, 2003 | ||||
3+1 quadruplex ([GGGTTA]2GGGT) | 2AQY | Zhang et al, 2005 | ||||
quadruplex (AAA[GGGTTA]3GGGAA) | 2HY9 | Dai et al, 2007 | ||||
anti/parallel quadruplex (AGGG[TTAGGG]3) | 2E4I | Matsugami et al, 2007 | ||||
quadruplex (TT[AGGGTT]4) | 2JPZ | Dai et al, 2007 | ||||
Bombyx mori (domestic silkworm) | quadruplex (TAGG) | 1AFF | Kettani et al, 1997 | |||
Tetrahymena thermophila | quadruplex (TTGGGG)4 | 186D | Wang et al, 1994 | |||
Oxytricha nova (Sterkiella nova) | 4 stranded quadruplex (GGGGTTTTGGGG) | 1D59 | Kang et al, 1992 | |||
dimeric quadruplex (GGGGTTTTGGGG) | 156D | |||||
dimeric quadruplex (GGGGTTTTGGGG) K+ form | 1K4X | Schultze et al, 1999 | ||||
quadruplex (GGGG[TTTTGGGG]3) | 201D | Wang et al, 1995 | ||||
quadruplex (GGGGTTTTGGGG) | 1JPQ | Haider et al, 2002 | ||||
thallium form quadruplex (GGGGTTTTGGGG) | 2HBN | Gill et al, 2006 | ||||
unimol. quadruplex ([G]4TUTU[G]4[T]4[G]4UUTT[G]3I) | 230D | Smith et al, 1995 | ||||
Viral Reverse Transcriptases |
HIV-1 | RT, DNA/RNA douplex complex | 1HYS | Sarafianos et al, 2001 | ||
RT, DNA/DNA douplex, tenofovir-diphosphate bound | 1T05 | Tuske et al, 2004 | ||||
MMLV (Moloney Murine Leukemia Virus) | RT (catalytic domain) | 1MML | Georgiadis et al, 1995 | |||
RT (N-terminal domain), dsDNA complex | 1D0E | Najmudin et al, 2000 | ||||
RT, (integrase processing site), dsDNA complex | 2FVS | MontaƱo et al, 2006 |