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SWIB/MDM2 domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SWIB/MDM2 domain [ 47591]
Superfamily:   SWIB/MDM2 domain [ 47592]
Families:   SWIB/MDM2 domain [ 47593] (4)


Superfamily statistics
Genomes (666) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,452 7,876 10
Proteins 3,075 7,212 10


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organonitrogen compound metabolic process 0.202 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.09473 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.368 Least Informative Inherited
Biological Process (BP) biological regulation 0.00446 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.001324 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.0493 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.3245 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0.0000000001837 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000000003716 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000001091 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00007796 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0006051 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.09303 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.5362 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.02148 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2231 Moderately Informative Inherited
Biological Process (BP) regulation of cell cycle 0.06251 Informative Inherited
Biological Process (BP) circulatory system development 0.01311 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.01983 Informative Inherited
Biological Process (BP) cellular component disassembly 0.00000001525 Highly Informative Direct
Biological Process (BP) heart development 0.0002123 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.1387 Highly Informative Inherited
Molecular Function (MF) binding 0.000001545 Least Informative Direct
Molecular Function (MF) transferase activity 0.6091 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000003166 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.0001277 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.0005838 Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.000101 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.0001019 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0001625 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0003995 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0009855 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.001284 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000002592 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000009325 Moderately Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.000000000009144Moderately InformativeDirect
Biological processUbl conjugation pathway0.000000004398Moderately InformativeDirect
Biological processNeurogenesis0.00000001656InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing0.00000004007Least InformativeDirect
DomainZinc-finger0.00000000000005219Moderately InformativeDirect
Molecular functionZinc0.00000001646Least InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationInitiation factor0.00000001334InformativeDirect
Post-translational modificationPhosphoprotein0.00000004332Least InformativeDirect
Post-translational modificationUbl conjugation0.0000000000005064Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0001184Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003121 SSF47592 Protein matches
Abstract

The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation [PubMed11147808]. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [PubMed12016060], and can be found fused to the C-terminus of DNA topoisomerase in Chlamydia.

MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription [PubMed8875929]. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain.

The SWIB and MDM2 domains are homologous and share a common fold.


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-coverage) · 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 5 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 SWIB/MDM2 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 5 hidden Markov models representing the SWIB/MDM2 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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]