Volume 17, Issue 1, Pages 137-143 (January 2005) Mammalian SCAN Domain Dimer Is a Domain-Swapped Homolog of the HIV Capsid C- Terminal Domain  Dmitri Ivanov, James R. Stone, Jenny L. Maki, Tucker Collins, Gerhard Wagner  Molecular Cell  Volume 17, Issue 1, Pages 137-143 (January 2005) DOI: 10.1016/j.molcel.2004.12.015

Figure 1 Structure of the SCAN Dimer (A and B) Family of the 20 lowest-energy NMR structures of SCAN dimer looking down the C2 symmetry axis. Two halves of the dimer, aligned separately in (B), are fairly well determined, but the global rmsd is higher due to uncertainty in the relative angle between the two halves. (C and D) Differential labeling method used to determine the dimer interface. Selected strips from a 15N-dispersed NOESY spectrum. (C) The 100% deuterated, 15N-labeled SCAN domain contained no NOE crosspeaks between the hydrogen-exchanged backbone amide protons and deuterated aliphatic hydrogens. (D) Same experiment after the deuterated sample is dimer exchanged with a sample of unlabeled protein. The mixed heterodimer contains additional crosspeaks to aliphatic protons of the nondeuterated monomer. Amide proton assignments are provided at the bottom of each 2D slice and the crosspeaks assignments are indicated within the spectrum. Intermonomer contacts were observed for a total of 20 backbone amides of each monomer (residues shown in green in (A) and (B)) (see Experimental Procedures). (E) Crosseye stereo view along the C2 symmetry axis. The ribbons of the two monomers are colored red and blue. Shown in yellow are the hydrophobic residues forming a symmetric hydrophobic core in the center of the structure. Five helical segments are marked H0 through H4, N and C termini are also annotated. Shown in green are two symmetry-related hydrophobic cores between helices H2, H3, and H4. Other important hydrophobic residues of the dimer interface are shown in black. Several interface residues are labeled for reference. Molecular Cell 2005 17, 137-143DOI: (10.1016/j.molcel.2004.12.015)

Figure 2 SCAN Domain Is Related to Retroviral Capsid C-Terminal Domains (A) Primary sequence alignment of ZNF174 SCAN domain and four retroviral CTDs based on the structural alignment of these highly homologous structures. Numbering of α helices follows the numbering proposed for HIV-1 CTD (Gamble et al., 1997). Viral capsid structures contain about one turn of a 310 helix in place of “Helix 0” of the SCAN domain. (B) Right half of the SCAN dimer from Figure 1E (red and blue) compared with the structure of the C-terminal domain of HIV-1 capsid protein (magenta, PDB code 1a43). Helical segments are marked H0 to H4. Tyr54 of ZNF174 and Phe161 of HIV-1 capsid both form part of the hydrophobic core between helices H2, H3, and H4. (C) Comparison of HIV-1 Gag-Pol polyprotein and vertebrate SCAN-containing proteins. Abbreviations are: matrix, MA; capsid, CA; nucleocapsid, NC; protease, PR; integrase, IN; and reverse transcriptase, RT. In lower vertebrates, SCAN-like domains appear in predicted retroviral-like polyproteins (BAB83836 locus in Oryzias latipes is shown as an example). Shown in green are regions of sequence homology with retroviral enzymes, and CCHC zinc knuckles are marked in blue. Close structural homologs SCAN and capsid C-terminal domain are colored red. Molecular Cell 2005 17, 137-143DOI: (10.1016/j.molcel.2004.12.015)

Figure 3 3D Domain Swapping and Its Proposed Role in Retroviral Assembly (A) Schematic of the SCAN dimer and the HIV capsid CTD dimer illustrating dimerization by domain swapping. The individual monomers are colored blue and red. The MHR fold is highlighted. (B) Ribbon diagrams of the SCAN dimer (left) and the HIV capsid CTD dimer (PDB code 1a43). Shown in yellow are the key hydrophobic residues of the dimer interfaces. W184 and M185 of HIV-1 are labeled. Shown in green are additional hydrophobic residues that would form the dimer interface in the SCAN-like domain-swapped structure of the HIV-1 capsid CTD. Side chains of residues important for HIV assembly Q155, K158, and D197 are shown in magenta. The disulfide bridge between Cys198 and Cys218 is also shown. (C) Model for the role of CTD dimerization in the HIV assembly. Initial Gag-Gag contacts are formed due to interactions mediated by Gag regions outside of CTD. These interactions most likely involve MA and NC domains and may require myristyl group, association with plasma membrane, and RNA binding. The conformational restraints imposed by these interactions destabilize the monomeric form of CTD and drive the subsequent formation of the tight domain-swapped CTD dimer. Abbreviations: capsid N-terminal domain, NTD; spacer peptide 1, SP1; otherwise same as previously indicated. Molecular Cell 2005 17, 137-143DOI: (10.1016/j.molcel.2004.12.015)