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(-) Description

Title :  EXTENDED SID OF MAD1 BOUND TO THE PAH2 DOMAIN OF MSIN3B
 
Authors :  H. Van Ingen, E. Lasonder, J. F. Jansen, A. M. Kaan, C. A. Spronk, H. G. Stunnenberg, G. W. Vuister
Date :  19 May 03  (Deposition) - 20 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (30x)
Keywords :  Pah2, Sin3, Mad1, Eukaryotic Transcriptional Regulation, Protein-Protein Interactions (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Van Ingen, E. Lasonder, J. F. Jansen, A. M. Kaan, C. A. Spronk, H. G. Stunnenberg, G. W. Vuister
Extension Of The Binding Motif Of The Sin3 Interacting Domain Of The Mad Family Proteins(, ).
Biochemistry V. 43 46 2004
PubMed-ID: 14705930
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIN3B PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T
    Expression System Strain: PBL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PAH2 DOMAIN (RESIDUES 148-232)
    Gene: SIN3
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - MAD1
    Chains: B
    Engineered: YES
    Fragment: EXTENDED SID DOMAIN (RESIDUES 5-28)
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PD7)

(-) Sites  (0, 0)

(no "Site" information available for 1PD7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PD7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PD7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PD7)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002644444aENSE00001885295chr2:70142203-70142535333MAD1_HUMAN1-25251B:198-21821
1.5aENST000002644445aENSE00001646891chr2:70143253-70143352100MAD1_HUMAN25-58341B:218-2214
1.6ENST000002644446ENSE00001006489chr2:70148868-7014889730MAD1_HUMAN58-68110--
1.7ENST000002644447ENSE00000759552chr2:70162483-70162597115MAD1_HUMAN68-106390--
1.8bENST000002644448bENSE00000759553chr2:70164367-70164526160MAD1_HUMAN107-160540--
1.9cENST000002644449cENSE00000846481chr2:70165229-701700774849MAD1_HUMAN160-221620--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:85
 aligned with SIN3B_MOUSE | Q62141 from UniProtKB/Swiss-Prot  Length:1098

    Alignment length:85
                                   157       167       177       187       197       207       217       227     
          SIN3B_MOUSE   148 ESDSVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFRGQEDLLSEFGQFLPEAKR 232
               SCOP domains d1pd7a_ A: Sin3B                                                                      SCOP domains
               CATH domains 1pd7A00 A:1-85  [code=1.20.1160.11, no name defined]                                  CATH domains
               Pfam domains ------------------------PAH-1pd7A01 A:25-81                                      ---- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1pd7 A   1 ESDSVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFRGQEDLLSEFGQFLPEAKR  85
                                    10        20        30        40        50        60        70        80     


Chain B from PDB  Type:PROTEIN  Length:24
 aligned with MAD1_HUMAN | Q05195 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:24
                                    14        24    
           MAD1_HUMAN     5 VRMNIQMLLEAADYLERREREAEH  28
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
           Transcript 1 (1) Exon 1.4a            --- Transcript 1 (1)
           Transcript 1 (2) --------------------1.5a Transcript 1 (2)
                 1pd7 B 198 VRMNIQMLLEAADYLERREREAEH 221
                                   207       217
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: PAH] (7)

(-) Gene Ontology  (29, 35)

NMR Structure(hide GO term definitions)
Chain A   (SIN3B_MOUSE | Q62141)
molecular function
    GO:0001106    RNA polymerase II transcription corepressor activity    Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0005515    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).
    GO:0003714    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.
biological process
    GO:0048738    cardiac muscle tissue development    The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0000122    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.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007519    skeletal muscle tissue development    The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016580    Sin3 complex    A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
    GO:0000805    X chromosome    The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.
    GO:0001741    XY body    A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
    GO:0000806    Y chromosome    The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males.
    GO:0030849    autosome    Any chromosome other than a sex chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B   (MAD1_HUMAN | Q05195)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0005515    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).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0003714    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.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007275    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).
    GO:0000122    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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MAD1_HUMAN | Q05195: 1e91 1g1e 1nlw 1s5q
        SIN3B_MOUSE | Q62141: 1e91 2cr7 2czy 2f05

(-) Related Entries Specified in the PDB File

5457 COMPLETE 1H CHEMICAL SHIFT ASSIGNMENT OF THE EXTENDED SID OF MAD1 BOUND TO THE PAH2 DOMAIN OF MSIN3B
1e91 NMR STRUCTURE OF MINIMAL SID OF MAD1 BOUND TO PAH2 DOMAIN OF MSIN3B
1g1e NMR STRUCTURE OF MINIMAL SID OF MAD1 BOUND TO PAH2 DOMAIN OF MSIN3A