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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 (2,993) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 21,767 112,951 31
Proteins 21,702 112,492 31

Functional annotation
General category Information
Detailed category Translation

Function annotation of SCOP domain superfamilies

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the head0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0000001605Least InformativeDirect
Worm Phenotype (WP)cell development variant0.00000127Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000008444Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.002526Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.002948Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.006817Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.2327Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.000000000006434Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.000003691Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00004411Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00004508Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0001894Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0005668Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.001594Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.002573Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.003339Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.005225Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.08152Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.09524Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.4162Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.5346Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.857Moderately InformativeInherited
Worm Phenotype (WP)cell number increased0.00000000000005027InformativeDirect
Worm Phenotype (WP)VPC competence variant0.000000000008363InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000007431InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000008942InformativeDirect
Worm Phenotype (WP)sick0.000000008973InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000001189InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0000001564InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.00003324InformativeDirect
Worm Phenotype (WP)reduced brood size0.0000374InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000106InformativeDirect
Worm Phenotype (WP)vulva development variant0.0002069InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.0004084InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0007927InformativeDirect
Worm Phenotype (WP)cell stress response variant0.001227InformativeInherited
Worm Phenotype (WP)pattern protein expression variant0.002808InformativeInherited
Worm Phenotype (WP)endosome morphology variant0.003544InformativeInherited
Worm Phenotype (WP)mitosis variant0.03496InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.6084InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.00000000003183Highly InformativeDirect
Worm Phenotype (WP)recycling endosome localization variant0.000001207Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.00003425Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.00006125Highly InformativeDirect
Worm Phenotype (WP)organism heat response variant0.0001265Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0001825Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.0002783Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.0003058Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.0004508Highly InformativeDirect
Worm Phenotype (WP)unfolded protein response variant0.0004865Highly 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)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0.01413Least InformativeInherited
Xenopus ANatomical entity (XAN)germ line cell0.0008723Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00007601InformativeDirect

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

InterPro annotation
Cross references IPR010920 SSF50182 Protein matches

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 · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]