The Structure of the Human Adenovirus 2 Penton Chloe Zubieta, Guy Schoehn, Jadwiga Chroboczek, Stephen Cusack  Molecular Cell  Volume 17, Issue 1, Pages 121-135 (January 2005) DOI: 10.1016/j.molcel.2004.11.041

Figure 1 Sequence Alignment of Penton Base Proteins from Representative Adenovirus Serotypes and Subgroup Subgroup C Ad2, accession number PO3276; subgroup B Ad3, S41389; subgroup B Ad7, AAR89958; subgroup B Ad11, AAP49205; subgroup F Ad41, AAF14179; subgroup A Ad12, P36716; subgroup D Ad17, NP_049379; subgroup E Ad25, NP_478405; and subgroup D Ad37, CAC82544. The hypervariable RGD loop region (yellow), the variable loop (light green), residues involved in dodecahedron formation (blue), fiber peptide binding residues (pink), and residues implicated in detergent molecule binding (purple) are highlighted. Secondary structure elements are denoted above the sequence by blue arrows (β strands) and pink cylinders (α helices). Stars below the sequences denote completely conserved residues. The RGD sequence is highlighted in red. Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)

Figure 2 Adenovirus 2 Penton Base Dodecahedron (A) Electron micrographs of adenovirus 2 penton base (Ad2pb). The scale bar corresponds to 150 nm. Left, Ad2pb −49 construct after incubation for 1 hr in crystallization solution showing formation of dodecahedra. Right, Ad2pb −49 construct in a buffer of 25 mM Tris, (pH 7.5), and 100 mM NaCl showing the pentameric form. (B) Stereo view of a space-filling model of the dodecahedron looking down a 3-fold axis with each pentamer colored separately. The contact region between pentamers across the 2-fold axis is visible around the small triangular hole at the 3-fold axis. (C) Stereo view of the residues involved in dodecamerization. The surface is semitransparent with residues involved in the dodecahedron interface depicted as stick representations. The pentamer in red donates loops colored bright green (452–455), orange (58–61), and red (99–102), and the pentamer in blue donates 2-fold related loops colored in cyan (452–455), pink (58–61), and blue (99–102). Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)

Figure 3 Structure of the Adenovirus 2 Penton Base (A) Left, tricolor ribbon representation of the monomer with the jellyroll domain (green) and the insertion domain (blue, residues 129–434; red, residues 466–519). The termini are labeled N and C. The variable loop and the RGD loop are labeled with disordered residues 298–373 of the RGD loop depicted by a dotted line. Putative zwittergent 3-12 molecules are drawn as stick representations. Right, rainbow ribbon representation colored from N terminus (blue) to C terminus (red) viewed after rotation of approximately 90° from previous image. (B) Stereo view of the putative zwittergent 3-12 binding site on the penton base monomer. The detergent molecules are colored green. Interacting residues from the protein are cyan. (C) The pentamer, the functional unit of the penton base protein, shown as a surface representation (left) and ribbon diagram (right), with each monomer colored uniquely. The variable loop, RGD loop and N- and C termini are marked. Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)

Figure 4 Fiber Peptide Interactions with the Penton Base (A) Stereo diagram of the fiber peptide (red) bound to the penton base subunit interface viewed looking down the 5-fold axis. (B) Stereo view of the peptide binding site. The ribbon diagrams of the monomers are colored blue and green and the bound peptide is depicted as sticks with carbons colored white. Residues forming the peptide binding pocket are colored yellow for monomer A and orange for monomer B. Putative hydrogen bonding interactions are denoted by dashed yellow lines. (C) Stereo view of the experimental averaged electron density of the bound peptide. (D) Sequence alignment of the N-terminal portion of representative fiber proteins from serotypes Ad2, accession number P03275; Ad3, P04501; Ad7, AAR89975; Ad11, NP_852715; Ad12, DAA00575; Ad17, DAA00599; Ad25, NP_478420; Ad37, AAB71734; Ad41 short fiber, P16883; and Ad41 long fiber, P14267. Conserved residues (yellow) and the peptide sequence used for structural analysis (red) are highlighted. Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)

Figure 5 Structural Rearrangement of Ad2 Penton Base upon Fiber Peptide Binding (A) The pentamer without (left) and with (right) bound peptide shown as surface models. Colors are rainbow from N terminus (blue) to C terminus (red, not visible). At right, the peptide is colored dark blue. (B) Least squares structural alignment of Ad2pb and Ad2pb/fiber peptide complex showing conformational switch. The stereo ribbon diagram of the monomer is colored green for the jellyroll domain, blue for the first insertion, and red (uncomplexed) or yellow (complexed with peptide) for the second insertion domain. The carbon, oxygen, and nitrogen atoms of the fiber peptide are in cyan, red, and blue, respectively. (C) A passion fruit flower (Passiflora Purple Haze) that exhibits a natural occurrence of a 5-fold, 3-fold symmetry mismatch (see text). This photograph is reproduced with permission of Ulrich Katz, Botanical Garden Bochum, Germany. Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)

Figure 6 Structurally Related Viral Capsid Proteins Comparison of Ad2pb (left), the P1 domain of adenovirus 2 hexon (middle), and PRD1 P31 protein (equivalent to the penton base) (right). Each comprises a basic jellyroll domain with strands labeled conventionally B to I (top). Whereas P31 has no loop extensions, both hexon and penton base have complex and different elaborations arising from the DE loop (blue) and FG loop (red). The P2 domain of hexon, the PRD1 P3 protein (equivalent to hexon), and Vp54 from Paramecium bursaria have similar topologies (cf. Figure 3 in Nandhagopal et al. [2002] and Figure 4 in Benson et al. [1999]). Molecular Cell 2005 17, 121-135DOI: (10.1016/j.molcel.2004.11.041)