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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 (3,260) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 23,850 115,984 46
Proteins 23,685 115,625 46


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)biosynthetic process0.00005370Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.0000004350Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.0000019810Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0000097830.01231Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0070510.0000004973Least InformativeInherited
Biological Process (BP)primary metabolic process0.001930.0000000009896Least InformativeInherited
Biological Process (BP)peptide metabolic process00Moderately InformativeDirect
Biological Process (BP)gene expression0.00000000000002870Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000010860Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.0000000000000046470Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00000016790.000000004555Moderately InformativeDirect
Biological Process (BP)organelle organization0.0000072860.006901Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.039360.007087Moderately InformativeInherited
Biological Process (BP)ribosome biogenesis00InformativeDirect
Biological Process (BP)organelle assembly0.000000000021610.0000000000007794InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000000000000019010.0000000000004939InformativeDirect
Biological Process (BP)ribosome assembly0.00018280.00000000000006092Highly InformativeDirect
Molecular Function (MF)binding0.41931Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000031980.0000155Moderately InformativeDirect
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)RNA binding0.000000056290.00000000004925InformativeDirect
Cellular Component (CC)macromolecular complex0.000000000001930Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.000000000020620Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00054870.000000000001969Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000018580Least InformativeDirect
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part00Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit00InformativeDirect
Cellular Component (CC)cytosolic ribosome00.000001625InformativeDirect

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) biosynthetic 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 0.0000000009896 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000004973 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.01231 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000004555 Moderately Informative Direct
Biological Process (BP) organelle organization 0.006901 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.3805 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.007087 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.3168 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.4876 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.7397 Moderately Informative Inherited
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) organelle assembly 0.0000000000007794 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000000004939 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 1 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.002365 Informative Inherited
Biological Process (BP) regulation of cellular amide metabolic process 0.001076 Informative Inherited
Biological Process (BP) translational initiation 0.0000003633 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.0008381 Highly Informative Direct
Biological Process (BP) ribosome assembly 0.00000000000006092 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000155 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.00000000004925 Informative Direct
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000001969 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribosome 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0000004919 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00003925 Moderately Informative Direct
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0 Informative Direct
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.000001625 Informative Direct
Cellular Component (CC) nucleoplasm part 0.01211 Informative Inherited
Cellular Component (CC) plastid 0.002268 Informative Inherited
Cellular Component (CC) mitochondrial large ribosomal subunit 0 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 0.00000000000002638 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 variant0.000004881Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.000005983Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0001533Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002276Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0005192Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.00529Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.4756Least InformativeInherited
Worm Phenotype (WP)larval development variant0.4874Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.0000001439Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000007424Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000002682Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.001107Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.03278Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.08292Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.08724Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1747Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.0000000000001557InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000003InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000006545InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000000007629InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00000007566InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00000008238InformativeDirect
Worm Phenotype (WP)early larval arrest0.0005338InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.04076InformativeInherited
Worm Phenotype (WP)gonad vesiculated0.0000000008347Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000000002962Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000000008353Highly InformativeDirect
Worm Phenotype (WP)cell membrane organization biogenesis variant0.0004216Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0008611Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)heat sensitivity0.0008046InformativeDirect

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)integumentary system0Least InformativeDirect
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)cell0Moderately InformativeDirect
Zebrafish Anatomy (ZA)post-vent region0InformativeDirect
Zebrafish Anatomy (ZA)extension0Highly InformativeDirect

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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0.0003462Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005318Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.01075Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.07139Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.000001481InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.000003127InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00001451InformativeDirect
Xenopus ANatomical entity (XAN)limb0.00003272InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00007256InformativeDirect
Xenopus ANatomical entity (XAN)lung0.0001489InformativeDirect
Xenopus ANatomical entity (XAN)duct0.0007431InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.003049InformativeInherited
Xenopus ANatomical entity (XAN)connective tissue0.0129InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ0.06708InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.00007751Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation1Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentPlastid0.000000000000001304Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)protein biosynthesis0InformativeDirect

Document: UP 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]