Summary: Translation initiation factor 1A / IF-1
Translation initiation factor 1A / IF-1 Provide feedback
This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Internal database links
|SCOOP:||CDC48_N Myosin_N MtrA PRE_C2HC TOBE_2 DUF3898 Phage-tail_3 Prot_ATP_ID_OB RsgA_N|
|Similarity to PfamA using HHSearch:||RsgA_N|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006196
The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1.
The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined [PUBMED:9008164]. It displays some similarity with the cold shock domain (CSD) (INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site.
This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||translation initiation factor activity (GO:0003743)|
|RNA binding (GO:0003723)|
|Biological process||translational initiation (GO:0006413)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . 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 .
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
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Author:||Finn RD, Bateman A, Mistry J, Wood V|
|Number in seed:||431|
|Number in full:||21549|
|Average length of the domain:||63.80 aa|
|Average identity of full alignment:||64 %|
|Average coverage of the sequence by the domain:||80.97 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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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 eIF-1a domain has been found. There are 16 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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