1. Molecular Model of the Human 26S Proteasome
Paula C.A. da Fonseca, Jun He, Edward P. Morris 
Molecular Cell 
Volume 46, Issue 1, Pages (April 2012)
DOI: /j.molcel
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2. Molecular Cell 2012 46, 54-66DOI: (10.1016/j.molcel.2012.03.026)
Copyright © 2012 Elsevier Inc. Terms and Conditions

3. Figure 1 Three-Dimensional Map of the Human 26S Proteasome
Orthogonal surface representations of the three-dimensional map in side view.
Molecular Cell  , 54-66DOI: ( /j.molcel )
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4. Figure 2 Docking the 20S Core Subunits within the 26S Proteasome
(A–F) Sequential side view sections starting from surface shown in Figure 1 (left panel). 26S proteasome map is shown as gray mesh. Coordinates of individually docked subunits are represented as cartoons. Examples of regions where the H1 helices of the α and β subunits are well resolved are marked with closed and open arrows, respectively. The gating region of the α subunit ring is indicated in (E) with a dashed ellipse.
(G) Detail of map showing the good recovery of the secondary structure.
(H) α subunit ring and the gating region. Left panel shows side view central section of the 20S core. The gating region is characterized by two layers of density indicated by orange and green lines. Right panels show top view sections of the α subunit ring. Upper panel corresponds to the outer layer of the gating region and is centered on the H0 α helices. Arrows mark connections made between adjacent α subunits by the loops between the S2 and S3 β strands. Lower panel corresponds to the inner layer of the gating region.
Molecular Cell  , 54-66DOI: ( /j.molcel )
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5. Figure 3 Identification of the Rpt Subunits within the 26S Proteasome
(A) Semitransparent surface side view of the upper half of the 26S proteasome with fitted Rpt subunit coordinates represented as orange cartoons and the 20S core subunits in blue.
(B) Central section of map represented as gray mesh viewed as in (A) identifying the Rpt coiled-coil, OB, and C-terminal domains.
(C–E) Sequential cross-sections of map represented as gray mesh with the individual Rpt subunits identified and color coded. (C) AAA-ATPase domains. (D) OB domains. (E) Coiled-coil domains. The extension of the Rpt4-5 coiled coil beyond the docked coordinates is marked with a black arrow.
(F–J) Structure diagrams of the Rpt heterohexamer in side view (F–H) and top view (I and J): subunits are color coded as in (C)–(E).
(K) Top view of the interface between the Rpt heterohexamer and the 20S core α subunit ring. The C-terminal α helices of the Rpt homology models are shown as gray cartoons with their C termini in red. The C-terminal tails of the Rpt subunits are not modeled and extend 9–14 residues beyond the C-terminal helices.
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6. Figure 4 Identification of the Rpn2 Subunit
(A) Semitransparent surface side view of the upper half of the 26S proteasome as in Figure 3A showing fitted 20S core subunits (blue), fitted Rpt hexamer (orange), and Rpn2 coordinates (yellow).
(B) Section of map represented as gray mesh with fitted coordinates viewed as in (A).
(C) Section of the Rpn2 density with the fitted Rpn2 coordinates identifying the N-terminal domain (blue) and PC domain (yellow).
(D) Section of the Rpn2 PC domain density with fitted coordinates showing the outer, inner, and axial α helices (yellow) and the adjacent Rpt3-6 coiled coil.
(E) Interaction between Rpn2 PC domain (yellow) and the coiled-coil domains of Rpt3-6 (green). Green arrow indicates apparent extensions to the Rpt3-6 coiled coil.
Molecular Cell  , 54-66DOI: ( /j.molcel )
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7. Figure 5
Identification of Rpn1 Density and Helical Repeats of the 19S-RP
(A–C) Semitransparent surfaces with docked coordinates of the top half of the 26S proteasome map showing 20S core subunits (blue), Rpt heterohexamer (orange), Rpn2 (yellow), and helical repeats of the PCI subunits (green). (A) Map viewed with density assigned to Rpn1 (outlined with dashed ellipse) oriented toward the viewer. The front surface of the map is emphasized, and the rest is faded out in order to allow the Rpn1 density to be clearly distinguished from the rest of the 19S-RP. (B) Map viewed in the direction of the molecular 2-fold axis. (C) Map surface showing the extended ribbon-like densities assigned to helical repeats of PCI subunits.
Molecular Cell  , 54-66DOI: ( /j.molcel )
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8. Figure 6 Organization of the 19S-RP Lid
(A–E) Detailed sections of the 26S proteasome map (gray mesh) with docked homology model coordinates (cartoons). (A and B) Ribbon-like densities assigned to the PCI subunits which radiate in different directions. The closely integrated density in the center can be assigned to the winged helix domains of the subunits (arrowed). (C) Detail showing the interactions made by the N-terminal domain of Rpn6 with the α2 subunit of the 20S core and Rpt3. (D and E) Locations of the MPN subunits Rpn8 and Rpn11 and the ubiquitin receptor Rpn10.
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9. Figure 7 Molecular Model of the 26S Proteasome
(A–C) The map of the 26S proteasome (gray mesh) showing the 19S-RP viewed from different directions identifying the location of each of its subunits, in which fitted coordinates are shown as solid surfaces. Magenta dashed circles identify nonfitted densities that correspond to the N-terminal extensions of the Rpt4-5 subunit pair. In (C), a gray ellipse adjacent to Rpn2 indicates the binding site for Rpn13 (He et al., 2012).
(D) Molecular model of the 26S proteasome, where the main subunit domains are color coded.
(E) Diagram illustrating the overall arrangement of the 26S proteasome domains. Subunits represented in (D) are color coded as in (E).
Molecular Cell  , 54-66DOI: ( /j.molcel )
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