SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,985) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,572 81,719 31
Proteins 21,507 81,628 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)cellular aromatic compound metabolic process00Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00044550.002317Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)gene expression00Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.000000074770.000000002345Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.0000015960.000000005128Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.19950.1473Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.055450.04701Moderately InformativeInherited
Biological Process (BP)single-organism organelle organization0.79360.8695Moderately InformativeInherited
Biological Process (BP)RNA processing00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.000000000002120InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.0000012990.000002753InformativeDirect
Biological Process (BP)mitotic cell cycle0.1230.4292InformativeInherited
Biological Process (BP)cytoskeleton organization0.32180.09997InformativeInherited
Biological Process (BP)microtubule-based process0.054740.0003312InformativeInherited
Biological Process (BP)cell cycle process0.29920.8777InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process0.12280.08612InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)rRNA processing0.0000034620.0001804Highly InformativeDirect
Biological Process (BP)mRNA processing00Highly InformativeDirect
Biological Process (BP)RNA splicing00Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization00Highly InformativeDirect
Biological Process (BP)spindle organization0.0014330.001866Highly InformativeInherited
Molecular Function (MF)binding0.03410.8551Least InformativeInherited
Molecular Function (MF)nucleic acid binding00.0000000000005562Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)intracellular organelle part0.000000000000089630.0000000000001065Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.062910.08785Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.077040.08632Least InformativeInherited
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)transferase complex0.0000000770.000000003693Moderately InformativeDirect
Cellular Component (CC)spliceosomal complex00Highly InformativeDirect
Cellular Component (CC)small nucleolar ribonucleoprotein complex0.0000030330.00000000007927Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex0.00041980.0003195Highly InformativeDirect
Cellular Component (CC)cytoplasmic ribonucleoprotein granule0.0000000000049980Highly 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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.002317 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000002345 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.000000005128 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.1473 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04701 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9927 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.8695 Moderately Informative Inherited
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) microtubule-based process 0.0003312 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000002753 Informative Direct
Biological Process (BP) organelle assembly 0.008722 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.9509 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.08036 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.09997 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.4292 Informative Inherited
Biological Process (BP) cell cycle process 0.8777 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.002763 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.08612 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) rRNA processing 0.0001804 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0.00006694 Highly Informative Direct
Biological Process (BP) RNA splicing 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Highly Informative Direct
Biological Process (BP) spindle organization 0.001866 Highly Informative Inherited
Molecular Function (MF) binding 0.8551 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000000000005562 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.4642 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) gated channel activity 0.18 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.0000000000001065 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.08632 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.08785 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.000000003693 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.1347 Informative Inherited
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) small nucleolar ribonucleoprotein complex 0.00000000007927 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.00008768 Highly Informative Direct
Cellular Component (CC) nuclear body 0.00001825 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0.0003195 Highly Informative Direct
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0006805Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004778Least InformativeInherited
Worm Phenotype (WP)growth variant0.6646Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.000000000903Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.0000002312Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00002447Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000489Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.00009095Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000126Moderately InformativeDirect
Worm Phenotype (WP)cell death variant0.003144Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.004011Moderately InformativeInherited
Worm Phenotype (WP)VPC competence variant0.000000000003978InformativeDirect
Worm Phenotype (WP)sick0.000000006581InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000007676InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000001601InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0000002516InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.000003521InformativeDirect
Worm Phenotype (WP)protein expression variant0.0001238InformativeDirect
Worm Phenotype (WP)brood size variant0.0003806InformativeDirect
Worm Phenotype (WP)vulva development variant0.0003874InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0005688InformativeDirect
Worm Phenotype (WP)cell division variant0.03473InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.4437InformativeInherited
Worm Phenotype (WP)cell corpse number variant0.4769InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.000000000000003737Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.000000008142Highly InformativeDirect
Worm Phenotype (WP)protein subcellular localization variant0.00000004034Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.00004441Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.000121Highly InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.0006577Highly InformativeDirect
Worm Phenotype (WP)germline proliferation variant0.6633Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.5161Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.2443InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)embryo0.001171Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.1299Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.0003265Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0004679InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0.0006646Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0006859Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0008606Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processStress response0InformativeDirect
Biological processmRNA splicing0InformativeDirect
Biological processTranslation regulation0.0000005124InformativeDirect
Biological processrRNA processing0.0000005306InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIon channel0.0000000000002122InformativeDirect

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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]