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: 19.22 kDa 
• Atom Count: 1356 
• Modelled Residue Count: 169 
• Deposited Residue Count: 169 
• Unique protein chains: 2

2LD7

Solution structure of the mSin3A PAH3-SAP30 SID complex

• PDB DOI: 10.2210/pdb2LD7/pdb
• BMRB: 17653

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


• Deposited: 2011-05-16 Released: 2011-06-15 
• Deposition Author(s): Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., Radhakrishnan, I.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding.

Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., Radhakrishnan, I.

(2011) J Biol Chem 286: 27814-27824

• PubMed: 21676866 
• DOI: 10.1074/jbc.M111.252494
• Primary Citation of Related Structures:  
  2LD7


• PubMed Abstract: 
  

The ∼2-megadalton evolutionarily conserved histone deacetylase-associated Rpd3L/Sin3L complex plays critical roles in altering the histone code and repressing transcription of a broad range of genes involved in many aspects of cellular physiology. Targeting of this complex to specific regions of the genome is presumed to rely on interactions involving one or more of at least 10 distinct subunits in the complex. Here we describe the solution structure of the complex formed by the interacting domains of two constitutively associated subunits, mSin3A and SAP30. The mSin3A paired amphipathic helix 3 (PAH3) domain in the complex adopts the left-handed four-helix bundle structure characteristic of PAH domains. The SAP30 Sin3 interaction domain (SID) binds to PAH3 via a tripartite structural motif, including a C-terminal helix that targets the canonical PAH hydrophobic cleft while two other helices and an N-terminal extension target a discrete surface formed largely by the PAH3 α2, α3, and α3' helices. The protein-protein interface is extensive (∼1400 Å(2)), accounting for the high affinity of the interaction and the constitutive association of the SAP30 subunit with the Rpd3L/Sin3L complex. We further show using NMR that the mSin3A PAH3-SAP30 SID complex can bind to nucleic acids, hinting at a role for a nucleolar localization sequence in the SID αA helix in targeting the Rpd3L/Sin3L complex for silencing ribosomal RNA genes.

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Organizational Affiliation: 

Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase complex subunit SAP30	A	94	Mus musculus	Mutation(s): 0  Gene Names: Sap30
UniProt & NIH Common Fund Data Resources
Find proteins for O88574 (Mus musculus) Explore O88574  Go to UniProtKB:  O88574
IMPC:  MGI:1929129

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Paired amphipathic helix protein Sin3a	B	75	Mus musculus	Mutation(s): 0  Gene Names: Sin3a, Kiaa4126
UniProt
Find proteins for Q60520 (Mus musculus) Explore Q60520  Go to UniProtKB:  Q60520

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LD7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-16 
• Released Date: 2011-06-15 
Deposition Author(s): Xie, T., He, Y., Korkeamaki, H., Zhang, Y., Imhoff, R., Lohi, O., Radhakrishnan, I.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-04
  Changes: Database references