General Information

Database Accession: DI1010008

Name: MAD1-Sin3B Interaction

PDB ID: 1e91 PDB

Experimental method: NMR

Source organism: Homo sapiens / Mus musculus

Proof of disorder: Confirmed

K_d: 1.40×10^-06 M PubMed

Primary publication of the structure:

Spronk CA, Tessari M, Kaan AM, Jansen JF, Vermeulen M, Stunnenberg HG, Vuister GW
The Mad1-Sin3B interaction involves a novel helical fold.
(2000) Nat. Struct. Biol. 7: 1100-4

PMID: 11101889 PubMed

Abstract:

Sin3A or Sin3B are components of a corepressor complex that mediates repression by transcription factors such as the helix-loop-helix proteins Mad and Mxi. Members of the Mad/Mxi family of repressors play important roles in the transition between proliferation and differentiation by down-regulating the expression of genes that are activated by the proto-oncogene product Myc. Here, we report the solution structure of the second paired amphipathic helix (PAH) domain (PAH2) of Sin3B in complex with a peptide comprising the N-terminal region of Mad1. This complex exhibits a novel interaction fold for which we propose the name 'wedged helical bundle'. Four alpha-helices of PAH2 form a hydrophobic cleft that accommodates an amphipathic Mad1 alpha-helix. Our data further show that, upon binding Mad1, secondary structure elements of PAH2 are stabilized. The PAH2-Mad1 structure provides the basis for determining the principles of protein interaction and selectivity involving PAH domains.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

transcription corepressor activity Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery. GeneOntology

protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GeneOntology

Biological process:

negative regulation of transcription from RNA polymerase II promoter Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. GeneOntology

transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GeneOntology

multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GeneOntology

Cellular component:

cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GeneOntology

nuclear chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. GeneOntology

nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: B, A

Notes: No modifications of the original PDB file.

Chain B

Name: Max dimerization protein 1 Disordered Confirmed

Source organism: Homo sapiens

Length: 13 residues

Sequence:Sequence according to PDB SEQRESNIQMLLEAADYLE

UniProtKB AC: Q05195 (positions: 8-20) UniProt Coverage: 5.9%

UniRef90 AC: UniRef90_Q05195 (positions: 8-20) UniRef90

Chain A

Name: Paired amphipathic helix protein Sin3b Ordered

Source organism: Mus musculus

Length: 85 residues

Sequence:Sequence according to PDB SEQRESESDSVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFRGQEDLLSEFGQFLPEAKR

UniProtKB AC: Q62141 (positions: 148-232) UniProt Coverage: 7.7%

UniRef90 AC: UniRef90_Q62141 (positions: 148-232) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain B: Disordered Confirmed

The 8-20 region described in IDEAL entry IID00165 covers 100% of the sequence present in the structure. The protein region involved in the interaction contains a known functional linear motif (LIG_Sin3_1).

Chain A: Ordered

The PAH domain involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF02671). A solved monomeric structure of the domain is represented by PDB ID 2f05.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There is 1 related structure in the Protein Data Bank:

• 1pd7

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