Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.08 kDa 
• Atom Count: 921 
• Modelled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 2

1PD7

Extended SID of Mad1 bound to the PAH2 domain of mSin3B

• PDB DOI: 10.2210/pdb1PD7/pdb
• BMRB: 5808
• BMRB: 5457

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-19 Released: 2004-01-20 
• Deposition Author(s): Van Ingen, H., Lasonder, E., Jansen, J.F., Kaan, A.M., Spronk, C.A., Stunnenberg, H.G., Vuister, G.W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Extension of the binding motif of the sin3 interacting domain of the mad family proteins(,).

Van Ingen, H., Lasonder, E., Jansen, J.F., Kaan, A.M., Spronk, C.A., Stunnenberg, H.G., Vuister, G.W.

(2004) Biochemistry 43: 46-54

• PubMed: 14705930 
• DOI: 10.1021/bi0355645
• Primary Citation of Related Structures:  
  1PD7


• PubMed Abstract: 
  

Sin3 forms the scaffold for a multiprotein corepressor complex that silences transcription via the action of histone deacetylases. Sin3 is recruited to the DNA by several DNA binding repressors, such as the helix-loop-helix proteins of the Mad family. Here, we elaborate on the Mad-Sin3 interaction based on a binding study, solution structure, and dynamics of the PAH2 domain of mSin3 in complex to an extended Sin3 interacting domain (SID) of 24 residues of Mad1. We show that SID residues Met7 and Glu23, outside the previously defined minimal binding motif, mediate additional hydrophobic and electrostatic interactions with PAH2. On the basis of these results we propose an extended consensus sequence describing the PAH2-SID interaction specifically for the Mad family, showing that residues outside the hydrophobic core of the SID interact with PAH2 and modulate binding affinity to appropriate levels.

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Organizational Affiliation: 

Departments of Biophysical Chemistry and Molecular Biology, NSRIM Center, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sin3b protein	A	85	Mus musculus	Mutation(s): 0  Gene Names: SIN3, Sin3b, Kiaa0700
UniProt
Find proteins for Q62141 (Mus musculus) Explore Q62141  Go to UniProtKB:  Q62141

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mad1	B	24	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q05195 (Homo sapiens) Explore Q05195  Go to UniProtKB:  Q05195
PHAROS:  Q05195 GTEx:  ENSG00000059728

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1PD7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-19 
• Released Date: 2004-01-20 
Deposition Author(s): Van Ingen, H., Lasonder, E., Jansen, J.F., Kaan, A.M., Spronk, C.A., Stunnenberg, H.G., Vuister, G.W.

Revision History  

• Version 1.0: 2004-01-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations