1. Structural Basis for the Specific Recognition of Methylated Histone H3 Lysine 4 by the WD-40 Protein WDR5 
Zhifu Han, Lan Guo, Huayi Wang, Yue Shen, Xing Wang Deng, Jijie Chai 
Molecular Cell 
Volume 22, Issue 1, Pages (April 2006)
DOI: /j.molcel
Copyright © 2006 Elsevier Inc. Terms and Conditions

2. Figure 1
Structure of the Complex between WDR5 and the Dimethylated H3-K4 Peptide
(A and B) Overall structure of the complex between WDR5 and the ten residue peptide is viewed from two perpendicular angles. The WDR5 molecule is shown in orange and the peptide in cyan. Oxygen and nitrogen atoms from the peptide are colored in blue and red, respectively. LME is for the residue of the dimethylated lysine in the peptide. The seven blades from WDR5 are numbered from 1 to 7, and the four strands from each blade are labeled A–D.
(C) Sequence alignment of WDR5 and Lis1ALFA2. Identical residues in both proteins are in white with red background, whereas the similar ones are in red with white background. Blue, green, and cyan squares identify those residues that are involved in hydrogen bonds, hydrophobic interactions, or both, respectively.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions

3. Figure 2
The Dimethylated H3-K4 Peptide Binds to the Top Surface of the WDR40 Repeat Domain in WDR5
(A) The omit density for the dimethylated peptide and E322 in WDR5 is shown in 1.1 sigma. The residues from the peptide and WDR5 are labeled. The green arrows indicate the positions of carbonyl oxygen atoms of the peptide. The map was calculated using the program CNS.
(B) A close-up view of the surface representation of the binding channel on the top of WDR5 for the dimethylated peptide. The blue, red, and white colors represent the positive, negative, and hydrophobic surfaces of WDR5, respectively.
(C) Close-up view of the interface between the first three residues, ART, from the dimethylated peptide and WDR5. The peptide is shown using a ball-and-stick representation. The side chains of those residues from WDR5 involved interactions with the peptide are shown in magenta. The dotted lines indicate the intermolecular hydrogen bonds between WDR5 and the peptide. The two red crosses represent the two water molecules.
(D) Stereo view of the interface between the dimethylated Lys4 in the peptide and WDR5. WDR5 and the peptide are shown in orange and green, respectively.
(E) Sequence alignment among the methylation sites plus their immediately preceding three residues from the N-terminal histones. The sequence of residues RHRK is from histone H4, and all the remaining ones are from histone H3. The number after K indicates the position of Lys in histone H3 or H4.
(F) Surface representation of peptide bound WDR5 is shown in orange, and the potential HMT binding site is highlighted in magenta.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions

4. Figure 3 Functional Consequences of Point Mutations in WDR5
Interaction of various WDR5 mutants with the 20 residue dimethylated peptide. A glutathione resin-mediated pull-down assay was used to assess the interaction between the 20 residue dimethylated peptide and various WDR5 mutants. The peptide dot blot analysis was used to detect the bound peptide as detailed in the Experimental Procedures.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions

5. Figure 4
The Superposition of WDR5 and Other WD40 Repeat-Containing Proteins Showing Overall Structural Similarity
(A) The molecules of WDR5 and Lis1ALFA2 are shown in orange and cyan, respectively. The side chains of those residues from WDR5 involved in the interaction with the peptide are colored in magenta.
(B) Different peptides bind at a similar position in different WDR40-repeat proteins. WDR5 and β-TrCp1 are shown in orange and green, respectively, and the WDR5 bound dimethylated peptide (MP) and the β-TrCp1 bound phosphorylated peptide (PP) are colored in red and pink, respectively.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2006 Elsevier Inc. Terms and Conditions