1KW4

Polyhomeotic SAM domain structure

• PDB DOI: https://doi.org/10.2210/pdb1KW4/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-01-28 Released: 2002-06-05 
• Deposition Author(s): Kim, C.A., Gingery, M., M Pilpa, R., Bowie, J.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.234 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

The SAM domain of polyhomeotic forms a helical polymer.

Kim, C.A., Gingery, M., Pilpa, R.M., Bowie, J.U.

(2002) Nat Struct Biol 9: 453-457

• PubMed: 11992127 
• DOI: https://doi.org/10.1038/nsb802
• Primary Citation of Related Structures:  
  1KW4


• PubMed Abstract: 
  

  The polycomb group (PcG) proteins are important in the maintenance of stable repression patterns during development. Several PcG members contain a protein protein interaction module called a SAM domain (also known as SPM, PNT and HLH). Here we report the high-resolution structure of the SAM domain of polyhomeotic (Ph). Ph-SAM forms a helical polymer structure, providing a likely mechanism for the extension of PcG complexes. The structure of the polymer resembles that formed by the SAM domain of another transcriptional repressor, TEL. The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.32 kDa 
• Atom Count: 607 
• Modelled Residue Count: 70 
• Deposited Residue Count: 89 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhomeotic	A	89	Drosophila melanogaster	Mutation(s): 3
UniProt
Find proteins for P39769 (Drosophila melanogaster) Explore P39769  Go to UniProtKB:  P39769

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.234 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.836	α = 90
b = 59.836	β = 90
c = 44.896	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-05 
Deposition Author(s): Kim, C.A., Gingery, M., M Pilpa, R., Bowie, J.U.

Revision History  

• Version 1.0: 2002-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations