1. Solution Structure of the Interacting Domains of the Mad–Sin3 Complex
Kurt Brubaker, Shaun M. Cowley, Kai Huang, Lenora Loo, Gregory S. Yochum, Donald E. Ayer, Robert N. Eisenman, Ishwar Radhakrishnan 
Cell 
Volume 103, Issue 4, Pages (November 2000)
DOI: /S (00)

2. Figure 1 Multiple Sequence Alignments of PAH and SID Domains
CLUSTAL W generated alignments of (A) the PAH2 domain of putative Sin3 homologues (top), the PAH domains of mSin3A (bottom), and (B) the PAH2-interacting SID domains from various species (prefix abbreviations: Hs: H. sapiens; Mm: M. musculus; Xl: X. laevis; Dm : D. melanogaster; Ce: C. elegans; Rn: R. norvegicus; and Dr: D. rerio). (C) Pairwise sequence alignments of minimal SID domains from Mad1 and Pf1 guided by the PAH2-interaction motif. Sequence identities (yellow) and similarities (green) are highlighted. Stars identify interfacial residues (i.e., those that contribute more than 1% and 5% of the interfacial area in the respective proteins) in the PAH2–SID complex. The sequence motif in (C) is given in the standard one-letter code for amino acids; φ = any bulky hydrophobic residue; X = any non-proline residue; and Z = any hydrophobic or polar/charged residue with a significant aliphatic component.
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3. Figure 2
1H-15N-Correlated Spectra of PAH2 and Intermolecular NOEs in the PAH2–SID Complex
Heteronuclear correlation maps of (A) free PAH2 and (B) PAH2 in the presence of an equivalent amount of SID. (C) Selected strips from a 3D 13C-filtered, 13C-edited NOESY spectrum depicting intermolecular NOEs. Incompletely suppressed signals from 13C-bound protons (diagonal peaks) are denoted by an “X”.
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4. Figure 3 Solution Structure of the PAH2–SID Complex
Stereo views of (A) the Cα trace of a best-fit superposition (involving backbone atoms in helical regions) of the ensemble of 14 NMR structures and (B) a ribbon diagram of the energy-minimized, average structure. The PAH2 domain is colored cyan while the SID peptide is shown in yellow.
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5. Figure 4
A Stereo View of the Hydrophobic Core of PAH2 in the PAH2–SID Complex
The side chains (gold) of residues belonging to α2, α3, α4 helices, and the C-terminal region of the α1 helix define the primary hydrophobic core.
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6. Figure 5 Interactions between PAH2 and SID
(A) A close-up view of the molecular surface of PAH2 is shown along with the interacting side chains (gold and magenta) of nonpolar residues of SID. The molecular surface is color coded according to curvature (gray: concave; white: flat; and green: convex). The SID peptide backbone (cyan) has been ghosted for clarity.
(B) Orthogonal views of the interacting helices of SID and PAH2 emphasizing the orientation of the αA helix (gold) relative to the α1 and α2 helices (blue). Apolar side chains (green) of SID and the molecular surface of PAH2 (purple mesh) that is within 2 Å of the molecular surface of SID are shown.
Cell  , DOI: ( /S (00) )

7. Figure 6
Noncovalent Interactions at the PAH2–SID Interface and Their Contributions to the Overall Stability of the Complex
(A) The side chains of PAH2 (gold) and SID (green) at the protein–protein interface are shown along with the respective polypeptide backbones (PAH2: cyan and SID: purple); noninteracting residues have been omitted for clarity.
(B) Binding activity of 35S-methionine labeled wild-type or mutant mSin3A to GST-SID (Mad1 residues 1–27) or GST in a GST-pulldown assay. Bound proteins were separated via gel electrophoresis. The input lane (1/5th) represents 20% of the total protein added to the experiment. The amount of wild-type or mutant mSin3A bound to GST-SID or GST was quantitated using a phosphoimager and expressed as a percentage of the 1/5th input for each protein.
Cell  , DOI: ( /S (00) )