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Sm-like ribonucleoproteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Sm-like fold [ 50181] (5)
Superfamily:   Sm-like ribonucleoproteins [ 50182] (6)
Families:   Sm motif of small nuclear ribonucleoproteins, SNRNP [ 50183] (8)
  Pleiotropic translational regulator Hfq [ 74939]
  Mechanosensitive channel protein MscS (YggB), middle domain [ 82090]
  PF1955-like [ 141294]
  LSM14 N-terminal domain-like [ 141297]
  YgdI/YgdR-like [ 159052] (6)


Superfamily statistics
Genomes (2,991) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 21,704 87,223 31
Proteins 21,639 86,892 31


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000000051370.0000000007218Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0048560.004307Least InformativeInherited
Biological Process (BP)biological regulation0.7071Least InformativeInherited
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)gene expression00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00000063110.000000000001326Moderately InformativeDirect
Biological Process (BP)cellular component assembly0.0015790.000004667Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.0000092060.00399Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.000011630.2333Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex subunit organization00InformativeDirect
Biological Process (BP)negative regulation of gene expression0.00000014010.00003433InformativeDirect
Biological Process (BP)mRNA processing00Highly InformativeDirect
Biological Process (BP)RNA splicing00Highly InformativeDirect
Molecular Function (MF)binding0.00076980.3752Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)intracellular organelle part0.000000000020170.0000001056Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.006660.008445Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.033960.02702Least InformativeInherited
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)transferase complex0.044260.05955Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.00015460.06446Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein granule0.0038350.0000000008627InformativeInherited
Cellular Component (CC)nucleoplasm part11InformativeInherited
Cellular Component (CC)small nuclear ribonucleoprotein complex00Highly InformativeDirect
Cellular Component (CC)SMN-Sm protein complex00Highly InformativeDirect
Cellular Component (CC)spliceosomal complex00Highly InformativeDirect
Cellular Component (CC)methylosome0.0000000000000026290Highly InformativeDirect
Cellular Component (CC)pole plasm0.00000029880Highly InformativeDirect
Cellular Component (CC)small nucleolar ribonucleoprotein complex0.0000051250.0000000001728Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex0.00030290.0002955Highly InformativeDirect
Cellular Component (CC)nuclear body0.00032390.0000216Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000007218 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.004307 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000000001326 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.000004667 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00399 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2333 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.7588 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8813 Moderately Informative Inherited
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00003433 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00002776 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0005533 Informative Direct
Biological Process (BP) organelle assembly 0.09014 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.03867 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.01102 Informative Inherited
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.007254 Highly Informative Inherited
Molecular Function (MF) binding 0.3752 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) passive transmembrane transporter activity 0.07297 Informative Inherited
Molecular Function (MF) gated channel activity 0.01682 Highly Informative Inherited
Molecular Function (MF) ion channel activity 0.04265 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.0000001056 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.02702 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.008445 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.05955 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.06446 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000008627 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) small nuclear ribonucleoprotein complex 0 Highly Informative Direct
Cellular Component (CC) SMN-Sm protein complex 0 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) methylosome 0 Highly Informative Direct
Cellular Component (CC) pole plasm 0 Highly Informative Direct
Cellular Component (CC) small nucleolar ribonucleoprotein complex 0.0000000001728 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0.0002955 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0000216 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processStress response0InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processrRNA processing0.0000001971InformativeDirect
Biological processTranslation regulation0.000001406InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationIon channel0.00000000000005922InformativeDirect
Post-translational modificationMethylation0.000001367Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010920 SSF50182 Protein matches
Abstract

This domain is found as the core structure in Lsm (like-Sm) proteins and bacterial Lsm-related Hfq proteins, and as the middle domain of the mechanosensitive channel protein MscS. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology.

Lsm proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [PubMed10801455, PubMed12438310]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. These snRNPs consist of seven Sm proteins (B/Bż, D1, D2, D3, E, F and G), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) [PubMed15130578]. Other snRNPs, such as U7 snRNP, can contain different Lsm proteins. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins.

The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA [PubMed12093755]. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.

The middle domain of the mechanosensitive channel of small conductance protein (MscS or YggB) structurally resembles an Lsm protein. MscS is a mechanosensitive channel present in the membrane of bacteria, archaea and eukarya that responds both to stretching of the cell membrane and to membrane depolarisation [PubMed12446901]. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region. The C-terminal cytoplasmic region can be further divided into middle and C-terminal domains, which together create a framework that connects to the cytoplasm through distinct openings. The middle domain exhibits an Lsm-like structure, consisting of five beta-strands that pack together with those of other subunits to form a barrel-like sheet extending around the entire protein.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 25 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Sm-like ribonucleoproteins domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 25 hidden Markov models representing the Sm-like ribonucleoproteins superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]