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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 (2,986) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,582 81,719 31
Proteins 21,517 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)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000000047770.0000000005446Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.015540.007663Least InformativeInherited
Biological Process (BP)gene expression00Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0002570.000001733Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.42240.2997Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.064020.0006395Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.10580.1028Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.000000094570InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.00017320.0008177InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.0029670.0001105InformativeInherited
Biological Process (BP)ncRNA processing11InformativeInherited
Biological Process (BP)RNA catabolic process0.00044530.00005815Highly InformativeDirect
Biological Process (BP)RNA splicing00Highly InformativeDirect
Biological Process (BP)mRNA metabolic process00Highly InformativeDirect
Biological Process (BP)rRNA metabolic process0.0000029590.0001818Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000000000000044090Highly InformativeDirect
Molecular Function (MF)binding0.00021790.2251Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000000000041620.000000000002243Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0610.05746Least InformativeInherited
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0070740.003415Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)transferase complex0.13850.1366Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein granule0.0013940.0000000001389InformativeInherited
Cellular Component (CC)spliceosomal complex00.000000000000007487Highly InformativeDirect
Cellular Component (CC)small nucleolar ribonucleoprotein complex0.0000012730.00000000002128Highly InformativeDirect
Cellular Component (CC)small nuclear ribonucleoprotein complex00Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex0.00032660.0002817Highly InformativeDirect
Cellular Component (CC)methylosome0.0000000000000054410Highly InformativeDirect
Cellular Component (CC)SMN-Sm protein complex00Highly InformativeDirect
Cellular Component (CC)pole plasm0.00000037990.000000000000003057Highly 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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000005446 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) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.007663 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) cellular component assembly 0.0006395 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000001733 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.1028 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2997 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6133 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 biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9031 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.0001944 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0002664 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0001105 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0008177 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.7365 Informative Inherited
Biological Process (BP) organelle assembly 0.01038 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.7203 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.6523 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.1117 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) RNA catabolic process 0.00005815 Highly Informative Direct
Biological Process (BP) RNA splicing 0 Highly Informative Direct
Biological Process (BP) mRNA metabolic process 0 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.0001818 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.00005882 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Highly Informative Direct
Molecular Function (MF) binding 0.2251 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 0.05679 Informative Inherited
Molecular Function (MF) gated channel activity 0.009064 Highly Informative Inherited
Molecular Function (MF) ion channel activity 0.03151 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.000000000002243 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.05746 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 0.003415 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.1366 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0265 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000001389 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.1116 Informative Inherited
Cellular Component (CC) spliceosomal complex 0.000000000000007487 Highly Informative Direct
Cellular Component (CC) small nucleolar ribonucleoprotein complex 0.00000000002128 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0.0002817 Highly Informative Direct
Cellular Component (CC) methylosome 0 Highly Informative Direct
Cellular Component (CC) SMN-Sm protein complex 0 Highly Informative Direct
Cellular Component (CC) pole plasm 0.000000000000003057 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the face0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the voice0.0008715InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.00000006105Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0000009973Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000006833Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.001619Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.001816Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.004328Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.000000000006053Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.000003368Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0000388Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000439Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0001821Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0006132Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.001541Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.003149Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.0052Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.432Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.8062Moderately InformativeInherited
Worm Phenotype (WP)cell number increased0.00000000000004257InformativeDirect
Worm Phenotype (WP)VPC competence variant0.000000000007257InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000000755InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000008796InformativeDirect
Worm Phenotype (WP)sick0.000000008955InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000001225InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0000001577InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.00003368InformativeDirect
Worm Phenotype (WP)brood size variant0.00006327InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.00009638InformativeDirect
Worm Phenotype (WP)vulva development variant0.0001928InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.0005648InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0008006InformativeDirect
Worm Phenotype (WP)pattern protein expression variant0.005534InformativeInherited
Worm Phenotype (WP)endosome morphology variant0.005823InformativeInherited
Worm Phenotype (WP)life span variant0.02926InformativeInherited
Worm Phenotype (WP)mitosis variant0.0436InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.451InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.00000000001439Highly InformativeDirect
Worm Phenotype (WP)protein subcellular localization variant0.00000004769Highly InformativeDirect
Worm Phenotype (WP)recycling endosome localization variant0.000001223Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.00003452Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.00006311Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0001793Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.0003069Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.0003108Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.0003253Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0007599Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.0002684Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0.07103Least InformativeInherited
Xenopus ANatomical entity (XAN)egg0.00005319Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0.06513Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00005585InformativeDirect

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 stage0.0006669Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0006883Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0008609Least 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 processing0InformativeDirect
Biological processrRNA processing0.0000009683InformativeDirect
Biological processTranslation regulation0.000001117InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIon channel0.0000000000004551InformativeDirect
Post-translational modificationMethylation0.0000009998Moderately 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) · Human Phenotype (HP) · Worm Phenotype (WP) · 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]