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392  structures 8824  species 0  interactions 83503  sequences 437  architectures

Family: S1 (PF00575)

Summary: S1 RNA binding 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]
Identifiers
SymbolS1
PfamPF00575
Pfam clanCL0021
InterProIPR003029
SMARTS1
PROSITEPDOC00053
MEROPSS15
SCOPe1sro / SUPFAM
CDDcd00164

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

  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. CiteSeerX 10.1.1.513.8431. doi:10.1016/j.jmb.2004.05.061. PMID 15312761.
  2. ^ 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.
This article incorporates text from the public domain Pfam and InterPro: IPR003029

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 RNA binding domain Provide feedback

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.

Literature references

  1. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG; , Cell 1997;88:235-242.: The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. PUBMED:9008164 EPMC:9008164


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003029

The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of proteins involved in RNA metabolism. It belongs to the OB-fold family. 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 [ PUBMED:9008164 , PUBMED:25430994 ].

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 [ PUBMED:9008164 ].

This entry does not include translation initiation factor IF-1 S1 domains.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 and the UniProtKB sequence database. More...

View options

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
(31)
Full
(83503)
Representative proteomes UniProt
(369938)
RP15
(12543)
RP35
(41166)
RP55
(82056)
RP75
(136799)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(31)
Full
(83503)
Representative proteomes UniProt
(369938)
RP15
(12543)
RP35
(41166)
RP55
(82056)
RP75
(136799)
Alignment:
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Download options

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
(31)
Full
(83503)
Representative proteomes UniProt
(369938)
RP15
(12543)
RP35
(41166)
RP55
(82056)
RP75
(136799)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 31
Number in full: 83503
Average length of the domain: 73.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 19.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 75
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Selections

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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 domain has been found. There are 392 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K283 View 3D Structure Click here
A0A0P0WPT1 View 3D Structure Click here
A0A0P0WPT1 View 3D Structure Click here
A0A0P0X3D3 View 3D Structure Click here
A0A0R0EVK5 View 3D Structure Click here
A0A0R0F511 View 3D Structure Click here
A0A0R0HVK1 View 3D Structure Click here
A0A0R0J7J3 View 3D Structure Click here
A0A0R0J7J3 View 3D Structure Click here
A0A0R0K588 View 3D Structure Click here
A0A1D6F3N9 View 3D Structure Click here
A0A1D6GYL6 View 3D Structure Click here
A0A1D6H4I5 View 3D Structure Click here
A0A1D6HD56 View 3D Structure Click here
A0A1D6HT49 View 3D Structure Click here
A0A1D6HV78 View 3D Structure Click here
A0A1D6HV78 View 3D Structure Click here
A0A1D6HV78 View 3D Structure Click here
A0A1D6JRH1 View 3D Structure Click here
A0A1D6JZL9 View 3D Structure Click here
A0A1D6KJR0 View 3D Structure Click here
A0A1D6LBR7 View 3D Structure Click here
A0A1D6MB51 View 3D Structure Click here
A0A1D6NKY4 View 3D Structure Click here
A0A1D6PBN3 View 3D Structure Click here
A0A1D6PBN3 View 3D Structure Click here
A0A1D6PCL1 View 3D Structure Click here
A0A1D8PGR5 View 3D Structure Click here
A0A1D8PGR5 View 3D Structure Click here
A0A1D8PGR5 View 3D Structure Click here
A0A1D8PGR5 View 3D Structure Click here
A0A1D8PP74 View 3D Structure Click here
A0A286Y8Y8 View 3D Structure Click here
A0A2R8QML1 View 3D Structure Click here
A1Z9L3 View 3D Structure Click here
A2A4P0 View 3D Structure Click here
A4HRY4 View 3D Structure Click here
B4G147 View 3D Structure Click here
B8JIP9 View 3D Structure Click here
B8JIP9 View 3D Structure Click here
B8JIP9 View 3D Structure Click here
C0H4U1 View 3D Structure Click here
C6T883 View 3D Structure Click here
C6T883 View 3D Structure Click here
D3ZCQ7 View 3D Structure Click here
D3ZNI3 View 3D Structure Click here
D3ZNI3 View 3D Structure Click here
D3ZNI3 View 3D Structure Click here
D3ZNI3 View 3D Structure Click here
D4A9B0 View 3D Structure Click here
F1LR36 View 3D Structure Click here
F1QI96 View 3D Structure Click here
F1QIX0 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
F4J8K6 View 3D Structure Click here
G3V6G7 View 3D Structure Click here
I1J7Z7 View 3D Structure Click here
I1J7Z7 View 3D Structure Click here
I1JFV5 View 3D Structure Click here
I1JFV5 View 3D Structure Click here
I1JFV5 View 3D Structure Click here
I1JFV5 View 3D Structure Click here
I1JFV5 View 3D Structure Click here
I1L0M6 View 3D Structure Click here
I1L0M6 View 3D Structure Click here
I1L0M6 View 3D Structure Click here
I1L4K9 View 3D Structure Click here
I1L4K9 View 3D Structure Click here
I1LMU3 View 3D Structure Click here
I1MGB0 View 3D Structure Click here
I1MGB0 View 3D Structure Click here
I1MGB0 View 3D Structure Click here
I1MZ01 View 3D Structure Click here
I1N5H9 View 3D Structure Click here
K7KNM0 View 3D Structure Click here
K7L4D0 View 3D Structure Click here
K7L4R5 View 3D Structure Click here
K7LD07 View 3D Structure Click here
K7LD07 View 3D Structure Click here
K7LD07 View 3D Structure Click here
K7LD07 View 3D Structure Click here
K7LKT8 View 3D Structure Click here
K7LKT8 View 3D Structure Click here
K7M8L9 View 3D Structure Click here
K7MHP3 View 3D Structure Click here
K7MHP3 View 3D Structure Click here
K7MP06 View 3D Structure Click here
K7N3Z8 View 3D Structure Click here
K7N3Z8 View 3D Structure Click here
O14459 View 3D Structure Click here
O42643 View 3D Structure Click here
O74835 View 3D Structure Click here
O74835 View 3D Structure Click here
O74835 View 3D Structure Click here
O74835 View 3D Structure Click here
P05055 View 3D Structure Click here
P05198 View 3D Structure Click here
P0A9J0 View 3D Structure Click here
P0AFF6 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P0AG67 View 3D Structure Click here
P20459 View 3D Structure Click here
P21499 View 3D Structure Click here
P21513 View 3D Structure Click here
P24384 View 3D Structure Click here
P30850 View 3D Structure Click here
P34087 View 3D Structure Click here
P34703 View 3D Structure Click here
P38421 View 3D Structure Click here
P41374 View 3D Structure Click here
P46279 View 3D Structure Click here
P46837 View 3D Structure Click here
P56286 View 3D Structure Click here
P62487 View 3D Structure Click here
P62488 View 3D Structure Click here
P62489 View 3D Structure Click here
P68101 View 3D Structure Click here
P9WH43 View 3D Structure Click here
P9WH43 View 3D Structure Click here
P9WH43 View 3D Structure Click here
P9WH43 View 3D Structure Click here
P9WI57 View 3D Structure Click here
Q05022 View 3D Structure Click here
Q05022 View 3D Structure Click here
Q05022 View 3D Structure Click here
Q09530 View 3D Structure Click here
Q09915 View 3D Structure Click here
Q0D7X0 View 3D Structure Click here
Q0DSD6 View 3D Structure Click here
Q0DSD6 View 3D Structure Click here
Q10MT2 View 3D Structure Click here
Q14562 View 3D Structure Click here
Q14690 View 3D Structure Click here
Q14690 View 3D Structure Click here
Q14690 View 3D Structure Click here
Q14690 View 3D Structure Click here
Q2FWJ5 View 3D Structure Click here
Q2FYF9 View 3D Structure Click here
Q2FYF9 View 3D Structure Click here
Q2FYF9 View 3D Structure Click here
Q2FYF9 View 3D Structure Click here
Q2FZ20 View 3D Structure Click here
Q2FZU8 View 3D Structure Click here
Q2G024 View 3D Structure Click here
Q2G0R3 View 3D Structure Click here
Q2G2D2 View 3D Structure Click here
Q2QP54 View 3D Structure Click here
Q38953 View 3D Structure Click here
Q497V5 View 3D Structure Click here
Q4CV69 View 3D Structure Click here
Q4E620 View 3D Structure Click here
Q54F05 View 3D Structure Click here
Q54L26 View 3D Structure Click here
Q54P04 View 3D Structure Click here
Q57581 View 3D Structure Click here
Q57840 View 3D Structure Click here
Q58598 View 3D Structure Click here
Q5A8Y7 View 3D Structure Click here
Q5AAU7 View 3D Structure Click here
Q5Z9X4 View 3D Structure Click here
Q5ZC75 View 3D Structure Click here
Q62383 View 3D Structure Click here
Q69LE7 View 3D Structure Click here
Q6ATY6 View 3D Structure Click here
Q6KAI0 View 3D Structure Click here
Q6NS46 View 3D Structure Click here
Q6NS46 View 3D Structure Click here
Q6NS46 View 3D Structure Click here
Q6NS46 View 3D Structure Click here
Q6Z7B3 View 3D Structure Click here
Q6ZWX6 View 3D Structure Click here
Q75LC0 View 3D Structure Click here
Q75LC0 View 3D Structure Click here
Q7KZ85 View 3D Structure Click here
Q7ZW41 View 3D Structure Click here
Q7ZWD3 View 3D Structure Click here
Q84NQ3 View 3D Structure Click here
Q869N9 View 3D Structure Click here
Q8GZQ3 View 3D Structure Click here
Q8IBH7 View 3D Structure Click here
Q8IJA4 View 3D Structure Click here
Q8IJC9 View 3D Structure Click here
Q8K1R3 View 3D Structure Click here
Q8N5C6 View 3D Structure Click here
Q8UVK2 View 3D Structure Click here
Q93VC7 View 3D Structure Click here
Q93VC7 View 3D Structure Click here
Q94AJ9 View 3D Structure Click here
Q9BKU3 View 3D Structure Click here
Q9ESX4 View 3D Structure Click here
Q9FE78 View 3D Structure Click here
Q9I9E9 View 3D Structure Click here
Q9LK47 View 3D Structure Click here
Q9LK47 View 3D Structure Click here
Q9M9H4 View 3D Structure Click here
Q9N3C9 View 3D Structure Click here
Q9N4L5 View 3D Structure Click here
Q9NP64 View 3D Structure Click here
Q9S7G6 View 3D Structure Click here
Q9SIZ2 View 3D Structure Click here
Q9SZD6 View 3D Structure Click here
Q9SZD6 View 3D Structure Click here
Q9VC94 View 3D Structure Click here
Q9VCX7 View 3D Structure Click here
Q9VFB5 View 3D Structure Click here
Q9W420 View 3D Structure Click here