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Zn-binding ribosomal proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Zn-binding ribosomal proteins [ 57829] (8)
Families:   Ribosomal protein L37ae [ 57830]
  Ribosomal protein L37e [ 57833]
  Ribosomal protein L44e [ 57836]
  Ribosomal protein S27e [ 90217]
  Ribosomal protein L32p [ 144200]
  Ribosomal protein L33p [ 144203]
  Ribosomal protein L40e [ 161181]
  Ribosomal protein S27a [ 161184]


Superfamily statistics
Genomes (3,217) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 12,239 52,932 32
Proteins 12,229 52,899 32


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 process0.0000000054450.00000000001133Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000000000017190.000000000002515Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.0000000000026870.0000000000112Least InformativeDirect
Biological Process (BP)primary metabolic process0.00000084040.0000003571Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0000019220.0002774Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00037290.00002369Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.75961Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.59420.9415Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.59980.9202Least InformativeInherited
Biological Process (BP)peptide metabolic process00Moderately InformativeDirect
Biological Process (BP)gene expression0.000000000000025970.0000000000000446Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000000000030350.00000000000002463Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.000000051590.00000000001889Moderately InformativeDirect
Biological Process (BP)organelle organization0.0028590.0006826Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.29910.8897Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.08590.0007417Moderately InformativeInherited
Biological Process (BP)ncRNA processing0.000000038340.00000006599InformativeDirect
Biological Process (BP)ribosome biogenesis00InformativeDirect
Biological Process (BP)organelle assembly0.000000000029570.0000000000001059InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000000025880.0000000002356InformativeDirect
Biological Process (BP)rRNA metabolic process0.00000000042990.0000000003256Highly InformativeDirect
Biological Process (BP)ribosome assembly0.00016010.0000000000121Highly InformativeDirect
Molecular Function (MF)binding0.96931Least InformativeInherited
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.00028060.0587Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0000096810.00007764InformativeDirect
Cellular Component (CC)macromolecular complex00Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.000017430.0000000261Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.00000070230.0000001135Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part00Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.053750.0000673Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.11830.08588Moderately InformativeInherited
Cellular Component (CC)mitochondrial ribosome0.00000000000037670.0000000000278InformativeDirect
Cellular Component (CC)large ribosomal subunit0.010950.1012InformativeInherited
Cellular Component (CC)mitochondrial large ribosomal subunit00.00000000000002499Highly 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) biosynthetic process 0.00000000001133 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000002515 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000000112 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000003571 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0002774 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00002369 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9415 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.9202 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0006826 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000000000446 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.0007417 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.00000000000002463 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00000000001889 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.8897 Moderately Informative Inherited
Biological Process (BP) ncRNA processing 0.00000006599 Informative Direct
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) organelle assembly 0.0000000000001059 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000002356 Informative Direct
Biological Process (BP) rRNA metabolic process 0.0000000003256 Highly Informative Direct
Biological Process (BP) ribosome assembly 0.0000000000121 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.0587 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00007764 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 0.0000000261 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000001135 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 0.0000673 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.08588 Moderately Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0.0000000000278 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.000004628 Informative Direct
Cellular Component (CC) large ribosomal subunit 0.1012 Informative Inherited
Cellular Component (CC) mitochondrial large ribosomal subunit 0.00000000000002499 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.002799Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.005543Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.007384Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03061Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00000002909Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.000000732Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0001191Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0002108Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.0006404Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0009302Moderately InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000000003368InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00000003913InformativeDirect
Worm Phenotype (WP)body width variant0.0001556InformativeDirect
Worm Phenotype (WP)RNA expression variant0.004366InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.02394InformativeInherited
Worm Phenotype (WP)RNA processing variant0.000002544Highly InformativeDirect
Worm Phenotype (WP)nonsense mRNA accumulation0.000005822Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.0000176Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least 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 cluster0.3845Least InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.005278Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.1087Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endomesoderm0InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0000002043InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.0001519InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.0007333InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0009903InformativeDirect
Xenopus ANatomical entity (XAN)connective tissue0.002567InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ0.01226InformativeInherited
Xenopus ANatomical entity (XAN)stomach0.0005291Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAntibiotic resistance0.0003671InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationIsopeptide bond0.00000004665Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011332 SSF57829 Protein matches
Abstract

This entry represents a rubredoxin-like metal-binding fold found in ribosomal proteins L37ae, L37e, L44e and S27e. This domain contains two CX(n)C motifs (where n is usually two) [PubMed15184028, PubMed15096641].


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) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 14 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 Zn-binding ribosomal proteins 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 14 hidden Markov models representing the Zn-binding ribosomal proteins 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) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]