Volume 8, Issue 2, Pages 455-463 (August 2001) Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus  Takuji Oyama, Yoshizumi Ishino, Isaac K.O. Cann, Sonoko Ishino, Kosuke Morikawa  Molecular Cell  Volume 8, Issue 2, Pages 455-463 (August 2001) DOI: 10.1016/S1097-2765(01)00328-8

Figure 1 Crystal Structure of P. furiosus RFCS (A) The overall fold of an RFCS subunit is shown by a ribbon representation. α helices and β strands are drawn by coils and arrows, respectively. The chain is colored cyan for Domain 1, green for Domain 2, and yellow for Domain 3. Walker A and B motifs are colored red. ADP is shown as a purple stick model. (B) The RFCS hexamer in the crystal is shown as a ribbon diagram viewed from the N-terminal side. The six subunits are colored blue, magenta, cyan, green, orange, and yellow-green for MolA to MolF, respectively. The four ADP molecules bound to MolA, MolB, MolC, and MolE are shown as red stick models. (C) A stereo view of an omit Fo-Fc electron density map contoured at 3 σ (ρ), drawn with ADP. Amino acid residues interacting with ADP are depicted. Water molecules are indicated by white spheres. (D) Orthogonal views of electrostatic potential mapped onto the molecular surfaces as calculated by the program GRASP (Nicholls and Honig, 1991). Positively charged surfaces are colored blue, and negatively charged surfaces are red. The figure in the upper left panel is viewed from the N-terminal side, as in (B). Trimer 1 (MolA to MolC) is indicated by a dotted line in the upper left (N-terminal side) and upper right (C-terminal side) panels Molecular Cell 2001 8, 455-463DOI: (10.1016/S1097-2765(01)00328-8)

Figure 2 Structure and Sequence Alignment among Clamp Loader Proteins (A) The structure of P. furiosus RFCS (left) is compared with that of E. coli δ′ (right) (Guenther et al., 1997). RFC boxes are colored in a rainbow gradation from box II (blue) to box VIII (red). ADP bound to P. furiosus RFCS is drawn as a stick model. The zinc atom in the E. coli δ′ structure is depicted by a pink sphere. (B) A multiple sequence alignment among clamp loader subunits. The nonconserved C-terminal regions of human RFC p140, P. furiosus RFCL, and E. coli γ are not shown in this alignment. The E. coli δ′ sequence was aligned manually, based on the crystal structure. Secondary structure assignments of RFCS are displayed over the sequences: helices are shown as cylinders, and strands are arrows with the same labeling as in Figure 1A on the cyan (Domain 1), green (Domain 2), and yellow (Domain 3) lines. Dashes in the sequences indicate gap positions. A number in parentheses within the human RFC p140 sequence refers to the number of inserted residues that are not shown in the alignment. Conserved residues in RFC boxes are highlighted by a magenta background, and other conserved residues against RFCS have a light green background. Abbreviations: RFCS, P. furiosus RFCS; HRFC140, HRFC40, HRFC38, HRFC37, and HRFC36: human RFC p140, p40, p38, p37, and p36, respectively; RFCL, P. furiosus RFCL; and GAMMA and DELTA′, E. coli γ and δ′, respectively Molecular Cell 2001 8, 455-463DOI: (10.1016/S1097-2765(01)00328-8)

Figure 3 Structure of RFCS Hexamers (A) Comparison of a hypothetical hexameric ring of RFCS (center) with the electron microscopic image (left). The 6-fold symmetry ring model was built from a semicircular trimer of RFCS in the crystal (right) and is drawn in top (upper) and side views (lower). One subunit in each hexamer is encircled. The EM 3D reconstructed images were obtained by essentially the same procedure as in our previous study (Mayanagi et al., 2001; K. Mayanagi and T. Miyata, personal communication). The scale bar indicated for the EM images is 50 Å. (B) Interaction scheme between subunits within the semicircular trimers, represented by an open-book view. Subunits with interfaces near the convex side of the crescent-shaped molecules are designated as “front,” while those with interfaces at the inner concave region of the crescents are designated as “back.” Only MolA and MolB are drawn as representative subunits. Segments contributing to the interfaces are colored blue for the front subunit and magenta for the back. In the front subunit, four segments, residues 4–14, 206–210, 229–231, and 262–271, contribute to Interface I (upper half), while two segments, residues 249–255 and 300–323, form Interface II (lower half). In the back subunit, residues 36–47 and 149–168 are involved in Interface I and residues 277–309 in Interface II. Intersubunit hydrogen bonding and hydrophobic interactions, which are observed in more than two interfaces of the total four, are indicated by red and green lines, respectively Molecular Cell 2001 8, 455-463DOI: (10.1016/S1097-2765(01)00328-8)