Summary: S1 domain
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S1 domain Edit Wikipedia article
S1 domain | |||||||||||
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Identifiers | |||||||||||
Symbol | S1 | ||||||||||
Pfam | PF00575 | ||||||||||
Pfam clan | CL0021 | ||||||||||
InterPro | IPR003029 | ||||||||||
SMART | S1 | ||||||||||
PROSITE | PDOC00053 | ||||||||||
MEROPS | S15 | ||||||||||
SCOPe | 1sro / SUPFAM | ||||||||||
CDD | cd00164 | ||||||||||
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The S1 domain is a protein domain that was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site.[2]
The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein.[2]
Function
The S1 domain is an essential in protein translation as it interacts with the ribosome and messenger RNA. S1 bind to RNA in a sequence specific manner.
Structure
This protein domain contains six motifs and 70 amino acids and it folds into a five-stranded antiparallel beta barrel. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site.[2]
References
- ^ Schubert M, Edge RE, Lario P, et al. (July 2004). "Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces". J. Mol. Biol. 341 (1): 37–54. CiteSeerX 10.1.1.513.8431. doi:10.1016/j.jmb.2004.05.061. PMID 15312761.
- ^ a b c Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG (January 1997). "The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold". Cell. 88 (2): 235–42. doi:10.1016/S0092-8674(00)81844-9. PMID 9008164.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
S1 domain Provide feedback
The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding.
Internal database links
SCOOP: | S1 |
Similarity to PfamA using HHSearch: | S1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR039566
This entry represents the S1 domain found in conserved virulence factor B proteins. The S1 domain has an OB-fold structure and is involved in nucleic acid binding.
Conserved virulence factor B proteins contribute to the expression of virulence factors and to pathogenicity via both agr-dependent and agr-independent pathways [PUBMED:17283102].
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 110 members:
BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF4539 DUF5666 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 Gp5_OB HIN ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_base_V Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB 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 Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OBAlignments
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 (58) |
Full (3165) |
Representative proteomes | UniProt (14472) |
NCBI (17938) |
Meta (75) |
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RP15 (366) |
RP35 (1563) |
RP55 (3146) |
RP75 (5797) |
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Jalview | |||||||||
HTML | |||||||||
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 (58) |
Full (3165) |
Representative proteomes | UniProt (14472) |
NCBI (17938) |
Meta (75) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (366) |
RP35 (1563) |
RP55 (3146) |
RP75 (5797) |
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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.
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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: | Jackhmmer:B5FDY3 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 58 |
Number in full: | 3165 |
Average length of the domain: | 61.00 aa |
Average identity of full alignment: | 31 % |
Average coverage of the sequence by the domain: | 30.63 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 61 | ||||||||||||
Family (HMM) version: | 7 | ||||||||||||
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 S1_2 domain has been found. There are 1 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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