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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 (3,255) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,772 100,252 46
Proteins 23,607 100,109 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 process0.00000350Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.0000015660Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.0000059760Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00000057970Least InformativeDirect
Biological Process (BP)primary metabolic process0.003370.000000002252Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.21820.02798Least InformativeInherited
Biological Process (BP)peptide metabolic process00Moderately InformativeDirect
Biological Process (BP)gene expression0.00000000000030690Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000000000000075480Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process00Moderately InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.00012770.00001171InformativeDirect
Molecular Function (MF)binding0.80711Least InformativeInherited
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.0011420.002754Moderately InformativeInherited
Molecular Function (MF)RNA binding0.00013440.00000002468InformativeDirect
Molecular Function (MF)structural constituent of ribosome00InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.00000000000072940Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.00000031450Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.001330.00000000001626Least InformativeInherited
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part00Moderately InformativeDirect
Cellular Component (CC)cytosolic large ribosomal subunit00.00000000000008495InformativeDirect

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 0.000000002252 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02798 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0001053 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) regulation of biosynthetic process 0.9093 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.9579 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.9359 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.00000007503 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00001171 Informative Direct
Biological Process (BP) cytoskeleton organization 1 Informative Inherited
Biological Process (BP) microtubule-based process 0.01627 Informative Inherited
Biological Process (BP) cell cycle process 0.1423 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.9174 Informative Inherited
Biological Process (BP) translational initiation 0.0000004077 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.002428 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.002754 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00000002468 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000001626 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) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribosome 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000001117 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000168 Moderately Informative Direct
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0 Informative Direct
Cellular Component (CC) cytosolic large ribosomal subunit 0.00000000000008495 Informative Direct
Cellular Component (CC) plastid 0.00625 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.02377 Informative Inherited
Cellular Component (CC) organellar large ribosomal subunit 0.767 Informative Inherited
Cellular Component (CC) transcription elongation factor complex 0.00000000000002307 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 variant0.000003096Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00005516Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0001143Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000222Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.000355Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.004975Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.4744Least InformativeInherited
Worm Phenotype (WP)larval development variant0.4876Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.0000001265Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000007971Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000001771Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000002735Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.001077Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.08657Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.08972Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1446Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.0000000000001524InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000003079InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000006832InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000000008201InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00000008092InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00000008443InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.04105InformativeInherited
Worm Phenotype (WP)gonad vesiculated0.0000000008186Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000000003117Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000000008709Highly InformativeDirect
Worm Phenotype (WP)cell membrane organization biogenesis variant0.0004174Highly InformativeDirect
Worm Phenotype (WP)early larval arrest0.0004698Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0008474Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)heat sensitivity0.0008125InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) 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 system0.000355Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005167Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.01037Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.07086Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.00000148InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.000003165InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.00001438InformativeDirect
Xenopus ANatomical entity (XAN)limb0.00003348InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00007369InformativeDirect
Xenopus ANatomical entity (XAN)lung0.0001516InformativeDirect
Xenopus ANatomical entity (XAN)duct0.0007406InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.002965InformativeInherited
Xenopus ANatomical entity (XAN)connective tissue0.01326InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ0.06715InformativeInherited
Xenopus ANatomical entity (XAN)oocyte0.00007856Highly 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 componentPlastid0.000000000000001298Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
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 ]