Summary: Telomere regulation protein Stn1
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Telomere regulation protein Stn1 Provide feedback
The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold [1]. This domain is the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [2].
Literature references
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Gao H, Cervantes RB, Mandell EK, Otero JH, Lundblad V; , Nat Struct Mol Biol. 2007;14:208-214.: RPA-like proteins mediate yeast telomere function. PUBMED:17293872 EPMC:17293872
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Martin V, Du LL, Rozenzhak S, Russell P; , Proc Natl Acad Sci U S A. 2007;104:14038-14043.: Protection of telomeres by a conserved Stn1-Ten1 complex. PUBMED:17715303 EPMC:17715303
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Gelinas AD, Paschini M, Reyes FE, Heroux A, Batey RT, Lundblad V, Wuttke DS;, Proc Natl Acad Sci U S A. 2009; [Epub ahead of print]: Telomere capping proteins are structurally related to RPA with an additional telomere-specific domain. PUBMED:19884503 EPMC:19884503
Internal database links
SCOOP: | tRNA_anti-codon |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018856
The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold [PUBMED:17293872]. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [PUBMED:17715303].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan OB (CL0021), which has the following description:
The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].
The clan contains the following 70 members:
BOF BRCA-2_OB1 BRCA-2_OB3 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CusF_Ec DNA_ligase_A_C DNA_ligase_OB DNA_ligase_OB_2 DUF1344 DUF2110 DUF223 DUF3127 DUF4539 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 MCM_OB mRNA_cap_C MRP-S35 NigD_N NlpE_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 Prot_ATP_ID_OB RecG_wedge RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bindAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (5) |
Full (326) |
Representative proteomes | UniProt (478) |
NCBI (830) |
Meta (1) |
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RP15 (46) |
RP35 (150) |
RP55 (238) |
RP75 (339) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (5) |
Full (326) |
Representative proteomes | UniProt (478) |
NCBI (830) |
Meta (1) |
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RP15 (46) |
RP35 (150) |
RP55 (238) |
RP75 (339) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_51291 (release 21.0) |
Previous IDs: | none |
Type: | Domain |
Author: | Mistry J, Wood V |
Number in seed: | 5 |
Number in full: | 326 |
Average length of the domain: | 133.30 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 41.97 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 252 | ||||||||||||
Family (HMM) version: | 8 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Stn1 domain has been found. There are 3 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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