1. Volume 13, Issue 10, Pages 1463-1472 (October 2005)
Two Different Conformational States of the KirBac3.1 Potassium Channel Revealed by Electron Crystallography 
Anling Kuo, Carmen Domene, Louise N. Johnson, Declan A. Doyle, Catherine Vénien-Bryan 
Structure 
Volume 13, Issue 10, Pages (October 2005)
DOI: /j.str
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2. Figure 1 Overview of the KirBac Structure
(A) Ribbon representation of two opposing KirBac1.1 monomers (out of four for clarity) showing the ion conduction pathway through the center of the channel. Inner helices are colored green, outer helices are purple, pore helices are gray, and slide helices are red. The red spheres represent K+ ions, and the Phe146 activation gate is shown as yellow sticks. Hinge points for both the inner and outer helices are indicated.
(B) Sequence alignment from the inner helices of the various K+ channels. The gating hinge glycine is colored in green, and the gating aromatic residue is colored in red.
Structure  , DOI: ( /j.str )
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3. Figure 2 2D Crystals of KirBac3.1 and Their Analysis
(A) Electron micrograph of KirBac3.1 crystal form 2 embedded in ice. Scale bar = 0.1 μm.
(B) Image-quality plot (IQ) of a single image of an orthorhombic frozen crystal. Each spot in the transform is represented by a square and a number (Henderson et al., 1986) indicating the signal to noise ratio. Smaller IQ values reflect higher-quality spots. Spots are shown to a resolution of 1/7 Å−1. The circles indicate the zero values of the phase contrast transfer function, and the axes give the directions of the reciprocal lattice vectors h and k.
(C) Purified protein was run on a 12% SDS-PAGE gel and stained with Coomassie brilliant blue. The standardized protein ladder is shown in the left lane.
Structure  , DOI: ( /j.str )
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4. Figure 3
Projection Maps of KirBac in Crystal Form 1 and Crystal Form 2 in Negative Staining and in Cryoconditions
(A and B) 2D projection map at low resolution of the crystals in negative staining conditions. (A) The closed conformation; one unit cell is outlined, a = 100 Å, b = 108 Å, γ = 90°. The 2-fold axes perpendicular to the membrane plane and the screw axes parallel to the membrane plane are indicated. In the bottom left, the protein KirBac3.1 is outlined. (B) The open conformation; unit cell dimensions are a = 100 Å, b = 110 Å, γ = 90°. In the bottom left, KirBac3.1 is outlined.
(C–F) 2D projection maps of KirBac3.1 from frozen specimen. (C) The closed conformation; one unit cell is outlined, a = 99 Å, b = 110 Å, γ = 90°. (D) The open state; unit cell dimensions are a = 99 Å, b = 114 Å, γ = 90°. Dashed contours represent density below the mean, and solid contours represent density above the mean. The contour interval is at about one-third of the root mean square density. (E) One KirBac3.1 in the closed conformation is shown. The two prominent intensity peaks inside one dimer are outlined (a and b) in gray circles, and the two less prominent intensity peaks are outlined (c and d) in white circles in the same dimer. Arrows are used for the other dimer. (F) One KirBac3.1 in the open conformation. Two sets of two high-density peaks are shown in one dimer: a′ and b′ in the gray circles and c′ and d′ in the white circles.
Structure  , DOI: ( /j.str )
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5. Figure 4 Fit of the 3D Model on the 2D Projection Map
(A–F) KirBac in the closed conformation. (A) Gray-level representation of the entire atomic model of KirBac1.1 filtered at 8 Å and projected in 2D. White represents high protein density. (B) Same as (A), using only the inner helices. The N- to C-terminal direction for two monomers is indicated with arrows. (C) Same as (A), using only the outer helices. (D) Same view as (A), but at atomic resolution. The inner and outer helices are in green and purple, respectively. (E) EM projection map of a single KirBac3.1 in the closed state with a ribbon representation of the inner helix in green superimposed. (F) Same as (E), but this time with the purple outer helices superimposed.
(G–J) KirBac in the open conformation. (G) Gray-level representation of the inner helices from the open model; N- to C-terminal direction for two monomers is indicated. (H) Gray-level representation of the open state’s outer helices. (I) EM projection map of the KirBac3.1 channel in the open state with a ribbon representation of the inner helices in green superimposed. (J) EM projection map of a KirBac3.1 protein in the open conformation, and ribbon representation of the outer helices in purple superimposed.
Structure  , DOI: ( /j.str )
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6. Figure 5 Overview of Gating Motions in KirBac3.1
(A) View of the transmembrane section of the closed conformation (top) and open conformation (bottom) from the extracellular side of the membrane. The outer helices (purple), the inner (green) helices, and the slide helices (red) are represented as ribbons. The Phe146 in the KirBac1.1 (Tyr132 in KirBac3.1) activation gate is displayed as yellow sticks.
(B) Two monomers of the closed channel (top) and open conformation channel (bottom) are shown superimposed upon a representation of the diameter of the central ion conduction pathway. Structural elements are colored as in Figure 1. Along the central ion conduction, the volume colored in red shows the place at which there is not enough space for a water molecule to pass; the volume in green shows where one or two water molecules could fit, and blue represents the volume where many water molecules can fit. Molecular graphics images were prepared with VMD (Humphrey et al., 1996).
Structure  , DOI: ( /j.str )
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