SUPERFAMILY 1.75 HMM library and genome assignments server


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 (648) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,292 3,363 10
Proteins 2,942 3,085 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) regulation of cellular process 7.629e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 0.1313 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001806 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.0182 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.7956 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1.381e-08 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.868e-08 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.664e-08 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.04498 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1359 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.00448 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.02685 Moderately Informative Inherited
Biological Process (BP) cellular component disassembly 2.941e-06 Informative Direct
Biological Process (BP) protein catabolic process 0.0008622 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 3.183e-09 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.06323 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.01117 Informative Inherited
Biological Process (BP) protein ubiquitination 5.285e-11 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.0001986 Highly Informative Direct
Biological Process (BP) regulation of G1/S transition of mitotic cell cycle 5.122e-08 Highly Informative Direct
Molecular Function (MF) binding 0.01599 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.009395 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 2.847e-05 Informative Direct
Molecular Function (MF) RNA binding 0.02096 Informative Inherited
Molecular Function (MF) transcription factor binding 0.0002226 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 2.375e-05 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 5.401e-06 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0005172 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.979e-06 Least Informative Direct
Cellular Component (CC) protein complex 0.2975 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01641 Least Informative Inherited
Cellular Component (CC) nuclear part 8.493e-10 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.03229 Moderately Informative Inherited
Cellular Component (CC) SWI/SNF superfamily-type complex 6.161e-15 Highly Informative Direct

Document: GO annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central 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)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately 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 regulation5.608e-12Moderately InformativeDirect
Biological processUbl conjugation pathway3.447e-09InformativeDirect
Biological processNeurogenesis9.6e-09InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing1.991e-08Least InformativeDirect
DomainZinc-finger7.2e-14Moderately InformativeDirect
Molecular functionZinc1.005e-08Least InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationInitiation factor1.462e-08InformativeDirect
Post-translational modificationPhosphoprotein1.131e-06Least InformativeDirect
Post-translational modificationUbl conjugation2.666e-12Moderately 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) · 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 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]