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0RRP5_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NamePDCD11
DescriptionRrp5 protein homolog (programmed cell death protein 11).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0005634 nucleus (IDA)
0008134 transcription factor binding (IPI)
0006915 apoptosis (ISS)
0043123 positive regulation of I-kappaB kinase/NF-k... (ISS)
0006355 regulation of transcription, DNA-dependent (ISS)
0006364 rRNA processing (ISS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
Ribosomes are the particles that catalyze mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain.ituated in the P site as peptidyl-tRNA.s then transferred to aminoacyl-tRNA and the new peptidyl-tRNA.xtended by one residue.s translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins.articularly those of the large subunit.re composed of a globular.urfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilize its structure. Most of the proteins interact with multiple RNA elements.ften from different domains. In the large subunit.bout 1/3 of the 23S rRNA nucleotides are at least in van der Waals contact with protein.nd L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7.hich initiate assembly of the 16S rRNA.re located at junctions of five and four RNA helices.espectively. In this way proteins serve to organize and stabilize the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based.roteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome.any ribosomal proteins have some function outside the ribosome .The S1 domain 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 . 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 .
  IPR003029:RNA binding S1
Ribosomes are the particles that catalyze mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain.ituated in the P site as peptidyl-tRNA.s then transferred to aminoacyl-tRNA and the new peptidyl-tRNA.xtended by one residue.s translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins.articularly those of the large subunit.re composed of a globular.urfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilize its structure. Most of the proteins interact with multiple RNA elements.ften from different domains. In the large subunit.bout 1/3 of the 23S rRNA nucleotides are at least in van der Waals contact with protein.nd L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7.hich initiate assembly of the 16S rRNA.re located at junctions of five and four RNA helices.espectively. In this way proteins serve to organize and stabilize the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based.roteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome.any ribosomal proteins have some function outside the ribosome .Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most.f not all.atural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase.nown to be phylogenetically related to S1) to degrade mRNA.r helper molecule involved in other RNase activities . Unique among ribosomal proteins.he primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other.
  IPR000110:Ribosomal protein S1
A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease andaspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1).nd has been termed the oligonucleotide/oligosaccharide binding motif.r OB fold. five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands . Two ribosomal proteins.17 and S1.re members of this class.nd have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case .There are many nucleic acid-binding proteins that contain domains with this OB-fold structure.ncluding anticodon-binding tRNA synthetases.NA helicases RecG and RuvA.sDNA-binding proteins (BRCA2.DC13.elomere-end binding proteins).hage ssDNA-binding proteins (gp32.p2.5.pV).old shock proteins.NA ligases.NA-capping enzymes.NA replication initiators and RNA polymerase subunit RBP8 .Please be aware that some of the protein hits may be false positives.
  IPR008994:Nucleic acid-binding, OB-fold
This domain consists of a multi-helical fold comprised of two curved layers of alpha helices arranged in a regular right-handed superhelix.here the repeats that make up this structure are arranged about a common axis . These superhelical structures present an extensive solvent-accessible surface that is well suited to binding large substrates such as proteins and nucleic acids. This topology has been found with a number of repeats and domains.ncluding the tetratricopeptide repeat (TPR) (found in kinesin light chains.NAP regulatory proteins.lathrin heavy chains and bacterial aspartyl-phosphate phosphatases).nd the pentatricopeptide repeat (PPR) (RNA-processing proteins). The TRP is likely to be an ancient repeat.ince it is found in eukaryotes.acteria and archaea.hereas the PPR repeat is found predominantly in higher plants. The superhelix formed from these repeats can bind ligands at a number of different regions.nd has the ability to acquire multiple functional roles .
  IPR011990:Tetratricopeptide-like helical
A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease andaspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1).nd has been termed the oligonucleotide/oligosaccharide binding motif.r OB fold. five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands . Two ribosomal proteins.17 and S1.re members of this class.nd have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case .This entry differs from Nucleic acid-binding OB-fold in the classification of the fold: both the NAD+-dependent DNA ligases.NA helicase RecG.nd the phage ssDNA-binding protein gp32 are absent from this classification.ut are found in the Nucleic acid-binding OB-fold.
  IPR012340:Nucleic acid-binding, OB-fold, subgroup
The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats).hough they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing . The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats ().eing of a similar length and consisting of two short helices connected by a loop domain.s in HEAT repeats.
  IPR003107:RNA-processing protein, HAT helix
IPR003029:S1 
Evalue:-18.7695510786217 
Location:540-611IPR003029:S1 
Evalue:-18.568636235841 
Location:727-798IPR003029:S1 
Evalue:-18.5528419686578 
Location:451-522IPR003029:S1 
Evalue:-12.7212463990472 
Location:1034-1109IPR003029:S1 
Evalue:-10.698970004336 
Location:1228-1298IPR003029:S1 
Evalue:-8.88605664769316 
Location:1322-1396IPR003029:S1 
Evalue:-7 
Location:185-258IPR003029:S1 
Evalue:-6.79588001734407 
Location:279-346IPR003029:S1 
Evalue:-6.67778070526608 
Location:363-436IPR003029:S1 
Evalue:-6.60205999132796 
Location:81-171IPR003029:S1 
Evalue:-4.2518119729938 
Location:634-707IPR003029:S1 
Evalue:-3.85387196432176 
Location:1147-1222IPR003107:HAT 
Evalue:-2.05551732784983 
Location:1705-1737IPR003107:HAT 
Evalue:-1 
Location:1775-1807IPR008994:Nucleic_acid_OB 
Evalue:0 
Location:845-970IPR000110:RIBOSOMALS1 
Evalue:0 
Location:0-0IPR003107:HAT 
Evalue:1.61278385671974 
Location:1633-1670IPR003107:HAT 
Evalue:1.67209785793572 
Location:1809-1844IPR003107:HAT 
Evalue:2.14612803567824 
Location:1739-1773IPR003107:HAT 
Evalue:2.81291335664286 
Location:1600-1631IPR003107:HAT 
Evalue:2.81291335664286 
Location:1672-1703
SequencesProtein: RRP5_HUMAN (1871 aa)
mRNA: NM_014976
Local Annotation
Synapse Ontology
A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
sdb:0039 positive regulation of long-term neuronal synaptic plasticity  (Evidence:keywords)
KO assignmentNot mapped to KEGG
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 26 residues, 105146401-105146477Exon2: 39 residues, 105148162-105148275Exon3: 46 residues, 105150143-105150275Exon4: 58 residues, 105152864-105153032Exon5: 56 residues, 105154768-105154930Exon6: 43 residues, 105155731-105155855Exon7: 62 residues, 105156355-105156537Exon8: 38 residues, 105159445-105159553Exon9: 71 residues, 105162862-105163069Exon10: 43 residues, 105163712-105163837Exon11: 22 residues, 105164016-105164077Exon12: 51 residues, 105164751-105164898Exon13: 86 residues, 105166237-105166489Exon14: 49 residues, 105167538-105167679Exon15: 67 residues, 105168186-105168381Exon16: 59 residues, 105169284-105169455Exon17: 75 residues, 105171094-105171314Exon18: 52 residues, 105172734-105172884Exon19: 40 residues, 105173289-105173405Exon20: 182 residues, 105174730-105175272Exon21: 23 residues, 105177075-105177138Exon22: 37 residues, 105181875-105181981Exon23: 32 residues, 105183694-105183784Exon24: 36 residues, 105183994-105184097Exon25: 61 residues, 105184544-105184722Exon26: 21 residues, 105187761-105187818Exon27: 43 residues, 105188432-105188555Exon28: 43 residues, 105189492-105189615Exon29: 99 residues, 105190036-105190328Exon30: 41 residues, 105190480-105190597Exon31: 52 residues, 105191572-105191722Exon32: 84 residues, 105191959-105192207Exon33: 58 residues, 105192911-105193080Exon34: 53 residues, 105193661-105193815Exon35: 57 residues, 105194263-105194429Exon36: 297 residues, 105195124-105196009Exon37: 2 residues, -Jump to RRP5_HUMAN  
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Loci Cluster (Details)Loci: 2632 105146401-105196009 ~-50K 5658(PDCD11)(+)Loci: 2631 105026909-105040091 ~-13K 5652(INA)(+)Link out to UCSC