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Translation proteins SH3-like domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   Translation proteins SH3-like domain [ 50104] (7)
Families:   Ribosomal proteins L24p and L21e [ 50105] (2)
  eIF5a N-terminal domain-like [ 50110] (3)
  C-terminal domain of ribosomal protein L2 [ 50114]
  N-utilization substance G protein NusG, C-terminal domain [ 82072]
  SPT5 KOW domain-like [ 141242]
  Ribosomal protein L19 [ 141245]
  Ribosomal protein L14e [ 159031]


Superfamily statistics
Genomes (3,262) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 24,080 149,447 46
Proteins 23,915 149,034 46


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
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 physiology variant0.000005363Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.000006565Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0001869Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002596Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0005872Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.005565Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.4658Least InformativeInherited
Worm Phenotype (WP)larval development variant0.4785Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.0000001478Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000008205Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000002861Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.03197Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.08642Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.08952Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1728Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.0000000000001556InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000003135InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000006763InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000000007879InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00000007916InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00000008435InformativeDirect
Worm Phenotype (WP)early larval arrest0.0005378InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.04116InformativeInherited
Worm Phenotype (WP)gonad vesiculated0.0000000008362Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000000003071Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000000862Highly InformativeDirect
Worm Phenotype (WP)cell membrane organization biogenesis variant0.000425Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0008314Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)heat sensitivity0.0008047InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)cell0Least InformativeDirect
Zebrafish Anatomy (ZA)post-vent region0InformativeDirect

Document: ZA 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)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0.3005Least InformativeInherited
Xenopus ANatomical entity (XAN)germ line cell0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.000424Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.0511Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.05778Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.000002024InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.000003039InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.0000139InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00002717InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0000612InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00009616InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.0014InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ0.03066InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.0001022Highly InformativeDirect
Xenopus ANatomical entity (XAN)bone tissue0.0002086Highly InformativeDirect
Xenopus DEvelopment stage (XDE)post-embryonic stage0.2239Least InformativeInherited
Xenopus DEvelopment stage (XDE)climax stage0.1226Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 660.0007813InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

InterPro annotation
Cross references IPR008991 SSF50104 Protein matches
Abstract

The fundamental activity of the ribosome is two-fold: to decode the message of the mRNA in the small subunit, and to form a peptide bond between peptidyl-tRNA and aminoacyl-tRNA by a peptidyl transferase activity in the large subunit. Several prokaryotic and eukaryotic proteins that are involved in the translation process contain an SH3-like domain. The structure of the translation protein SH3-like domain is a partly opened beta barrel, where the last strand is interrupted by a 3-10 helical turn. The structure of the RNA-binding C-terminal domain of the Bacillus stearothermophilus ribosomal protein L2 has been shown to adopt the SH3-like barrel topology [PubMed10075918]. The L2 protein is located near the peptidyl transferase centre in the large ribosomal subunit where it may contribute to peptidyl transferase activity, and is involved in the assembly of the 23SrRNA. Likewise, the N-terminal domain of the ubiquitous eukaryotic initiation translation factor 5a (IF-5A) protein adopts the SH3-like barrel topology [PubMed9724718, PubMed9753699]. IF-5A is involved in the initial step of peptide bond formation in translation and in cell-cycle regulation. IF-5A acts as a cofactor of the Rev protein in HIV-1-infected cells and of the Rex protein in T-cell leukaemia virus 1-infected cells.


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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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 23 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 Translation proteins SH3-like domain 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 23 hidden Markov models representing the Translation proteins SH3-like domain 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]