Telomerase Database-Structures

Component	Species	Structures	References
TR	Vertebrates	Homo sapiens (human)		.jpg	.pdf	Chen et al, 2000
Tupaia glis belangeri (common tree shrew)		.jpg	.pdf	Chen et al, 2000
Oryctolagus cuniculus (domestic rabbit)		.jpg	.pdf	Chen et al, 2000
Cavia porcellus (domestic guinea pig)		.jpg	.pdf	Chen et al, 2000
Chinchilla brevicaudata (short-tailed chinchilla)		.jpg	.pdf	Chen et al, 2000
Geomys breviceps (gopher)		.jpg	.pdf	Chen et al, 2000
Microtus ochrogaster (prairie vole)		.jpg	.pdf	Chen et al, 2000
Cricetulus griseus (Chinese hamster)		.jpg	.pdf	Chen et al, 2000
Mus musculus (mouse)		.jpg	.pdf	Chen et al, 2000
Rattus norvegicus (Norway rat)		.jpg	.pdf	Chen et al, 2000
Mustela putorius furo (domestic ferret)		.jpg	.pdf	Chen et al, 2000
Procyon lotor (raccoon)		.jpg	.pdf	Chen et al, 2000
Bos taurus (cattle)		.jpg	.pdf	Chen et al, 2000
Sus scrofa (pig)		.jpg	.pdf	Chen et al, 2000
Suncus murinus (Asian house shrew)		.jpg	.pdf	Chen et al, 2000
Equus caballus (domestic horse)		.jpg	.pdf	Chen et al, 2000
Dasypus novemcinctus (armadillo)		.jpg	.pdf	Chen et al, 2000
Dasyurus hallucatus (northern quoll)		.jpg	.pdf	Chen et al, 2000
Elephas maximus (Asian elephant)		.jpg	.pdf	Chen et al, 2000
Trichechus manatus (Caribbean manatee)		.jpg	.pdf	Chen et al, 2000

Anodorhynchus hyacinthinus (macaw)		.jpg	.pdf	Chen et al, 2000
Gallus gallus (chicken)		.jpg	.pdf	Chen et al, 2000

Chelydra serpentina (snapping turtle)		.jpg	.pdf	Chen et al, 2000

Bombina japonica (toad)		.jpg	.pdf	Chen et al, 2000
Xenopus laevis (African clawed frog)		.jpg	.pdf	Chen et al, 2000
Ceratophrys ornata (ornate horned frog)		.jpg	.pdf	Chen et al, 2000
Pyxicephalus adspersus (bull frog)		.jpg	.pdf	Chen et al, 2000
Dermophis mexicanus (Mexican caecilian)		.jpg	.pdf	Chen et al, 2000
Herpele squalostoma (Congo caecilians)		.jpg	.pdf	Chen et al, 2000
Typhlonectes natans (Rio Cauca caecilian)		.jpg	.pdf	Chen et al, 2000

Oryzias latipes (Medaka)		.jpg	.pdf	Xie et al, 2007
Takifugu rubripes (Fugu fish)		.jpg	.pdf	Xie et al, 2007
Danio rerio (zebrafish)		.jpg	.pdf	Xie et al, 2007
Rhizoprionodon porosus (sharpnose shark)		.jpg	.pdf	Chen et al, 2000
Dasyatis sabina (Atlantic stingray)		.jpg	.pdf	Chen et al, 2000
Rhinoptera bonasus (cownose ray)		.jpg	.pdf	Chen et al, 2000


Fungi	Saccharomyces cerevisiae (baker's yeast)		.jpg	.pdf	Brown et al, 2007 Dandjinou et al, 2004
Saccharomyces castellii		.jpg	.pdf	Brown et al, 2007 Dandjinou et al, 2004 Chappell and Lundblad, 2004
Kluyveromyces lactis		.jpg	.pdf	Brown et al, 2007 Chappell and Lundblad, 2004


Ciliates	Tetrahymena thermophila		.jpg	.pdf
Tetrahymena malaccensis		.jpg	.pdf
Tetrahymena pyriformis		.jpg	.pdf
Tetrahymena vorax		.jpg	.pdf
Tetrahymena borealis		.jpg	.pdf	McCormick-Graham et al, 1995
Tetrahymena silvana		.jpg	.pdf
Tetrahymena australis		.jpg	.pdf
Tetrahymena pigmentosa		.jpg	.pdf
Tetrahymena hyperangularis		.jpg	.pdf
Tetrahymena capricornis		.jpg	.pdf	McCormick-Graham et al, 1995
Tetrahymena hegewischi		.jpg	.pdf
Tetrahymena paravorax		.jpg	.pdf	McCormick-Graham et al, 1995
Paramecium tetraurelia		.jpg	.pdf	McCormick-Graham et al, 1996
Paramecium primaurelia		.jpg	.pdf
Paramecium multimicronucleatum		.jpg	.pdf	McCormick-Graham et al, 1996

Euplotes aediculatus		.jpg	.pdf	Lingner et al, 1994
Euplotes eurystomus		.jpg	.pdf	Lingner et al, 1994
Euplotes crassus		.jpg	.pdf	Lingner et al, 1994
Oxytricha nova (Sterkiella nova)		.jpg	.pdf	Lingner et al, 1994
Oxytricha trifallax (Sterkiella histriomuscorum)		.jpg	.pdf	Lingner et al, 1994
Stylonychia mytilis		.jpg	.pdf	Lingner et al, 1994
Stylonychia lemnae		.jpg	.pdf	Lingner et al, 1994

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
TR	Homo sapiens (human)	p2b hairpin	1NA2	.pdb	Theimer et al, 2003
		P2b, P3 pseudoknot	1YMO	.pdb	Theimer et al, 2005
		P2b hairpin (dyskeratosis congenita mutant)	1Q75	.pdb	Theimer et al, 2005
		P6 hairpin	1Z31	.pdb	Leeper et al, 2005
		P6.1 stem loop	1OQ0	.pdb	Leeper et al, 2003
		P8b hairpin	2QH2	.pdb	Theimer et al, 2007
	Tetrahymena thermophila	stem loop IV	2FEY	.pdb	Chen et al, 2006
		stem loop IV	2H2X	.pdb	Richards et al, 2006a
		helix II template boundary element	2FRL	.pdb	Richards et al, 2006b


TERT	Tribolium castaneum	catalytic subunit	3DU6	.pdb	Gillis et al, 2008
	Tetrahymena thermophila	TEN domain	2B2A	.pdb	Jacobs et al, 2006
	Tetrahymena thermophila	RNA binding domain	2R4G	.pdb	Rouda et al, 2007


Telomerase-associated Proteins	H/ACA ribonucleoprotein complex (dyskerin, Nop10, Gar1, NHP2)
	Pyrococcus furiosus	Cbf5, Nop10, Gar1, L7Ae, H/ACA RNA complex	2HVY	.pdb	Li et al, 2006
	Pyrococcus furiosus	Cbf5, Nop10, Gar1 complex	2EY4	.pdb	Rashid et al, 2006
	Pyrococcus abyssi	Cbf5, Nop10 complex	2AUS	.pdb	Manival et al, 2006
	Methanococcus jannaschii	Cbf5, Nop10 complex	2APO	.pdb	Hamma et al., 2005
	associated proteins
	Homo sapiens (human)	Est1A (Pin domain)	2DOK	.pdb	Tanokura et al, 2007
		Est1A (Pin domain)	2HWW	.pdb	Glavan et al, 2006
		Est1A (Pin domain, E1282C mutant)	2HWX	.pdb	Glavan et al, 2006
		Est1B (Pinc domain)	2HWY	.pdb	Glavan et al, 2006
	chaperones
	Homo sapiens (human)	hsp70 (N-terminal ATPase domain)	1HJO	.pdb	Osipiuk et al, 1999
		hsp70, hop (TPR1 domain) complex	1ELW	.pdb	Morshauser et al, 2000
		hsp90, hop (TPR2A domain) complex	1ELR	.pdb	Scheufler et al, 2000
		hsp90	1OSF	.pdb	Jez et al, 2003
	Bos taurus (cattle)	hsc70	1ATR	.pdb	O'Brien et al, 1993
	Rattus norvegicus (Norway rat)	hsc70 (substrate binding domain)	1CKR	.pdb	Zuiderweg et al, 1999
	Saccharomyces cerevisiae (yeast)	hsp40, hsp70 complex (C-terminal domains)	2B26	.pdb	Li et al, 2006
		hsp90, ATP complex	1AM1	.pdb	Prodromou et al, 1997
		hsp90, ADP copmlex	1AMW	.pdb	Prodromou et al, 1997
	Escherichia coli	DnaK (substrate binding domain)	1BPR	.pdb	Wang et al, 1998
	Escherichia coli	DnaK (substrate binding domain)	1DKZ	.pdb	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	.pdb	Lei et al, 2004
	Schizosaccharomyces pombe	Pot1, ssDNA complex	1QZH	.pdb	Lei et al, 2003
	telomeric repeat binding factors 1 and 2 (TRF1 and TRF2)
	Homo sapiens (human)	TRF1 (DNA binding domain), dsDNA complex	1IV6	.pdb	Nishikawa et al, 2001
		TRF1 (DNA binding domain), dsDNA complex	1W0T	.pdb	Rhodes et al, 2005
		TRF1 (DNA binding domain)	1BA5	.pdb	Nishikawa et al, 1998
		TRF1 (dimerization domain)	1H6O	.pdb	Fairall et al, 2001
		TRF1 (TRF domain), TIN2 (NL signal) complex	3BQO	.pdb	Chen et al, 2008
		TRF2 (dimerization domain)	1H6P	.pdb	Fairall et al, 2001
		TRF2 (DNA binding domain), dsDNA complex	1VFC	.pdb	Hanaoka et al, 2005
		TRF2 (DNA binding domain), dsDNA complex	1W0U	.pdb	Rhodes et al, 2005
		TRF2 (DNA binding domain)	1VF9	.pdb	Hanaoka et al, 2005
		TRF2 (C-terminal Myb domain)	1XG1	.pdb	Bilbille et al, 2006 (direct link)
	Nicotiana tabacum	TRF1 (DNA binding domain)	2CKX	.pdb	Cho et al, 2007 (to be published)
	Arabidopsis thaliana	TRP (DNA binding domain, like TRF)	2AJE	.pdb	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	.pdb	Wang et al, 2007
	TRF2-interacting protein (Rap1)
	Homo sapiens (human)	RAP1 (MYB domain)	1FEX	.pdb	Hanaoka et al, 2001
	Saccharomyces cerevisiae (yeast)	RAP1 (DNA-binding domain), dsDNA complex	1IGN	.pdb	Konig et al, 1996
	telomere binding protein (TBP)
	Oxytricha nova (Sterkiella nova)	TBP, ssDNA complex	1OTC	.pdb	Horvath et al, 1998
		TBP, ssDNA complex	2I0Q	.pdb	Buczek et al, 2006
		TBP, ssDNA complexed and uncomplexed	1K8G	.pdb	Classen et al, 2001
		TBP, ssDNA, DNA quadruplex complex	1JB7	.pdb	Horvath et al, 2001
		TBP, ssDNA, DNA quadruplex complex	1PA6	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH2	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH3	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH4	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH5	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH6	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH7	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH8	.pdb	Theobald et al, 2003
		TBP, ssDNA, DNA quadruplex complex	1PH9	.pdb	Theobald et al, 2003
		TBP (alpha subunit), ssDNA complex	1KIX	.pdb	Peersen et al, 2002
	telomere-associated proteins
	Saccharomyces cerevisiae (yeast)	Cdc13 (DNA binding domain)	1KXL	.pdb	Mitton-Fry et al, 2002
	Bombyx mori (domestic silkworm)	TRAS1 (N-terminal domain)	1WDU	.pdb	Maita et al, 2004


Telomeric DNA	Homo sapiens (human)	quadruplex (AGGG[TTAGGG]3)	143D	.pdb	Wang et al, 1993
		tetrad (AGGGT)	1EVM	.pdb	Patel et al, 1999
		quadruplex (TAGGGT)2	1K8P	.pdb	Parkinson et al, 2002
		parallel-stranded quadruplex (TTAGGGT)	1NZM	.pdb	Gavathiotis et al, 2003
		parallel-stranded quadruplex (TTAGGGT)	1NP9	.pdb	Gavathiotis et al, 2003
		3+1 quadruplex ([GGGTTA]2GGGT)	2AQY	.pdb	Zhang et al, 2005
		quadruplex (AAA[GGGTTA]3GGGAA)	2HY9	.pdb	Dai et al, 2007
		anti/parallel quadruplex (AGGG[TTAGGG]3)	2E4I	.pdb	Matsugami et al, 2007
		quadruplex (TT[AGGGTT]4)	2JPZ	.pdb	Dai et al, 2007
	Bombyx mori (domestic silkworm)	quadruplex (TAGG)	1AFF	.pdb	Kettani et al, 1997
	Tetrahymena thermophila	quadruplex (TTGGGG)4	186D	.pdb	Wang et al, 1994
	Oxytricha nova (Sterkiella nova)	4 stranded quadruplex (GGGGTTTTGGGG)	1D59	.pdb	Kang et al, 1992
		dimeric quadruplex (GGGGTTTTGGGG)	156D	.pdb	Smith et al, 1992 Schultze et al, 1994
		dimeric quadruplex (GGGGTTTTGGGG) K+ form	1K4X	.pdb	Schultze et al, 1999
		quadruplex (GGGG[TTTTGGGG]3)	201D	.pdb	Wang et al, 1995
		quadruplex (GGGGTTTTGGGG)	1JPQ	.pdb	Haider et al, 2002
		thallium form quadruplex (GGGGTTTTGGGG)	2HBN	.pdb	Gill et al, 2006
		unimol. quadruplex ([G]4TUTU[G]4[T]4[G]4UUTT[G]3I)	230D	.pdb	Smith et al, 1995


Viral Reverse Transcriptases	HIV-1	RT, DNA/RNA douplex complex	1HYS	.pdb	Sarafianos et al, 2001
	HIV-1	RT, DNA/DNA douplex, tenofovir-diphosphate bound	1T05	.pdb	Tuske et al, 2004
	MMLV (Moloney Murine Leukemia Virus)	RT (catalytic domain)	1MML	.pdb	Georgiadis et al, 1995
		RT (N-terminal domain), dsDNA complex	1D0E	.pdb	Najmudin et al, 2000
		RT, (integrase processing site), dsDNA complex	2FVS	.pdb	Montaño et al, 2006