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1  structure 8697  species 0  interactions 10019  sequences 9  architectures

Family: S1_2 (PF13509)

Summary: S1 domain

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This is the Wikipedia entry entitled "S1 domain". More...

S1 domain Edit Wikipedia article

S1 domain
PDB 1sn8 EBI.jpg
Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative).[1]
Symbol S1
Pfam PF00571
InterPro IPR003029
SCOP 1sn8

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]


  1. ^ 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. doi:10.1016/j.jmb.2004.05.061. PMID 15312761. 
  2. ^ a b 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. 

This article incorporates text from the public domain Pfam and InterPro IPR003029

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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.

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This tab holds annotation information from the InterPro database.

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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 49 members:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RsgA_N RuvA_N S1 S1-like S1_2 SSB SSL_OB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Seed source: Jackhmmer:B5FDY3
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 63
Number in full: 10019
Average length of the domain: 61.20 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 24.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 61
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 seqence.

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