Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid

“Cyclophilin A is (bonds) 5 0.005 Å; RMSD (angles) 5 1.38; there are no w,c angles required for the replication of group M human immunodeficiency in the forbidden range (Laskowski et al., 1993).”

“(B) and (C) were prepared with MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Bacon and Anderson, 1988). about CA151 residues 86 and 98, so that CypA and CA151 CypA active site groove.”

“Mode of action of SDZ NIM spersed with model building using O (Jones et al., 1991).”

“Schematic representation of the CA151 and CypA interface (Wallace et al., 1995).”

“Schreiber and Crabtree have proposed that CypA does not normally function as an enzyme in vivo However, it is possible that kcat/Km is similar to that of other substrates because kcat and Km have been(Schreiber and Crabtree, 1992).”

“The last six residues of both CA151 molecules are (A) Secondary structure of CA151 (Hutchinson and Thornton, 1996).”

“Molecular Recognition between CA151 and CypAprepared with MIDASPLUS (Ferrin et al., 1988).”

“Our face area is smaller than most stable protein–protein interfaces (Janin and Chothia, 1990), consistent with theCA151/CypA structure does not explain this observation, however, since each CypA makes specific contacts to modest dissociation constant of the CA/CypA complex.”

“Complex formation can also be inhibited by a series of mutations in the N-terminal The viral Gag protein and its proteolytically derived matdomain of CA (Franke et al., 1994b; Braaten et al., uration products serve as the major structural compo1996b).”

“(B) and (C) were prepared with MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Bacon and Anderson, 1988). about CA151 residues 86 and 98, so that CypA and CA151 CypA active site groove.”

“…replication is blocked at an early step fol- CA151 is a flat, tapered molecule with overall dimensionslowing penetration and cannot be rescued by CypA in of 18 Å 3 35 Å 3 45 Å and predominantly helical secondthe host cell (Thali et al., 1994; Braaten et al., 1996b). ary structure (Figure 1).”

“Thefor transporting rhodopsin through the endoplasmic reticulum and into the rhabdomere (Colley et al., 1991; superposition for CA151 improves to 0.43Å when residues 86–98 are omitted.”

“…Schutkowski et al., 1995; Zhao and Ke, 1996a; 90 N distance for both of the CA151/CypA complexes in the asymmetric unit is rather long (3.6 Å) in these groundZhao and Ke, 1996b) and that the protein exhibits little sequence specificity (Harrison and Stein, 1990b; Zhao state structures.”

“Overlap of CA151 Ca10-fold in vitro (reviewed in Schmid, 1993).”

“Phe-pNA appears to be a normal CypA substrate as judged by the kcat/Km ratio (Harrison and Stein, 1990b).”

“Capsid also 1994a), CA dimerization (Gitti et al., 1996), and viral as-binds the human peptidyl prolyl isomerase, cyclophilin sembly (Jowett et al., 1992; Dorfman et al., 1993; VonA, thereby packaging the enzyme into the virion.”

“Van der Waals interactions are defined as contacts ofThe CA151 Pro-90 residue binds to CypA in the same 4.1 Å or less in one of the two complexes. hydrophobic pocket as seen in all known CypA–peptide structures (Kallen et al., 1991; Ke et al., 1993; Zhao and Ke, 1996a; Zhao and Ke, 1996b).”

“Instead, the CA151/CypA structure exhib- its many of the features seen in the tight, specific com- rison and Stein, 1990a; Liu et al., 1990; Zhao and Ke, 1996a; Zhao and Ke, 1996b), but this is the first timeplex formed between CypA and cyclosporine, including hydrogen bonding interactions with the…”

“Upon maturation, the MA protein ubiquitiously expressed in the cytoplasm of eukaryotic lines the inner surface of the viral membrane while the cells (Koletsky et al., 1986), while other family members exhibit tissue- or organelle-specific expression patterns or can exist as discrete domains of…”

“…that affect Gag assembly generally map to the C-terminal third of CA (Jowett et al., 1992; Vona low affinity sequence, such as succinyl-Ala-Ala-transPro-Phe-pNA, begins to bind in the enzyme’s active site, Poblotzki et al., 1993; Dorfman et al., 1994; Franke et al., 1994a; Reicin et al., 1995).”

“Others have reported that the tetrapeptide succinyl-Ala-Gly-Pro-orientation in the CypA active site (Pflügl et al., 1993; Thériault et al., 1993).”

“Upon maturation, the MA protein ubiquitiously expressed in the cytoplasm of eukaryotic lines the inner surface of the viral membrane while the cells (Koletsky et al., 1986), while other family members exhibit tissue- or organelle-specific expression patterns or can exist as discrete domains of…”

“36 Å crystal structure of the N-terminal domain of man et al., 1993; Wang and Barklis, 1993; Franke etHIV-1 capsid (residues 1–151) in complex with human al., 1994b; Reicin et al., 1995).”

“…replication is blocked at an early step fol- CA151 is a flat, tapered molecule with overall dimensionslowing penetration and cannot be rescued by CypA in of 18 Å 3 35 Å 3 45 Å and predominantly helical secondthe host cell (Thali et al., 1994; Braaten et al., 1996b). ary structure (Figure 1).”

“…is competitively inhibited by mol-capsid strips, thereby promoting disassembly of the ecules that bind in the active site of CypA, including theviral core. immunosuppressive drug cyclosporine and its nonimmunosuppressive analog SDZ NIM 811 (Luban et al.,Introduction 1993; Billich et al., 1995).”

“…replication is blocked at an early step fol- CA151 is a flat, tapered molecule with overall dimensionslowing penetration and cannot be rescued by CypA in of 18 Å 3 35 Å 3 45 Å and predominantly helical secondthe host cell (Thali et al., 1994; Braaten et al., 1996b). ary structure (Figure 1).”

“…only residues within the N-terminal doreveals the sequence-specific interactions required for main that are invariant in an alignment of CA proteins HIV-1 packaging of CypA and suggests a mechanism for from a broad spectrum of retroviruses (McClure, 1991). the nonspecific rotamase activity of CypA.”

“In addition, 26 residues and 32 side chains throughout thecesses as the heat shock response (Sykes et al., 1993), cell surface recognition (Anderson et al., 1993), and vari- two complexes lack defined electron density and have been given an occupancy of zero for crystallographicous…”

“In addition, 26 residues and 32 side chains throughout thecesses as the heat shock response (Sykes et al., 1993), cell surface recognition (Anderson et al., 1993), and vari- two complexes lack defined electron density and have been given an occupancy of zero for crystallographicous…”

“Complex formation can also be inhibited by a series of mutations in the N-terminal The viral Gag protein and its proteolytically derived matdomain of CA (Franke et al., 1994b; Braaten et al., uration products serve as the major structural compo1996b).”

“…1.26 Å for CA151-2 whenpackage wild-type levels of the major viral proteins and RNAs, exhibit normal levels of endogenous reverse tran- regions that are mobile in solution are neglected. scriptase activity, and appear competent to enter cells (Steinkasserer et al., 1995; Braaten et al., 1996b).”

“In fact, their replication actually appears to be Gag protein is cleaved by the viral protease into three inhibited by CypA, since they require SDZ NIM 811 to new proteins: matrix (MA; 132 residues), capsid (CA; replicate in some cell lines (Aberham et al., 1996).”

“This change in accessible sur-It was recently reported that CypA binding depends on Gag or CA dimerization (Colgan et al., 1996).”

“Poblotzki et al., 1993; Reicin et al., 1995).”

“In the virion, was 0.7838. however, where the CA–CypA stoichiometry is 2000:200, 1994) using the 1.64 Å CypA structure of Ke et al. (1993) (PDB code affect viral replication in the presence of cyclopsorins.”

“The two CypA molecules in the asymmetric unit were located by molecular replacement with AMoRe(Navaza,out a role for the rotamase activity, it is not clear how an increase in the rate of isomerization of Pro-90 would CA strips, and it appears that binding of CypA sterically a measured as 318,604 partial and 8039 full…”

“In addition, 26 residues and 32 side chains throughout thecesses as the heat shock response (Sykes et al., 1993), cell surface recognition (Anderson et al., 1993), and vari- two complexes lack defined electron density and have been given an occupancy of zero for crystallographicous signalingpathways (Bramand Crabtree,…”

“…to the amide nitrogen of CA Pro-90 (Zhao and Ke, 1996a), although the Arg-55 Nh2 to Pro-Walkinshaw, 1992; Ke et al., 1993; Kakalis and Armitage, 1994; Schutkowski et al., 1995; Zhao and Ke, 1996a; 90 N distance for both of the CA151/CypA complexes in the asymmetric unit is rather long (3.6 Å) in…”

“Gag plays the central role in 1994b; Thali et al., 1994; Traber et al., 1994; Steinkasthis assembly process and can form budded, virus-like serer et al., 1995; Braaten et al., 1996b). particles in the absence of any other viral protein.”

“…and hydrogen bonding to the amide nitrogen of CA Pro-90 (Zhao and Ke, 1996a), although the Arg-55 Nh2 to Pro-Walkinshaw, 1992; Ke et al., 1993; Kakalis and Armitage, 1994; Schutkowski et al., 1995; Zhao and Ke, 1996a; 90 N distance for both of the CA151/CypA complexes in the asymmetric unit…”

“…A-Fc fragment 2.8 1300 2 Deisenhofer (1981) 1igc Protein G-Fab MOPC21 2.6 1350 14 Derrick & Wigley (1994) 1ak4 Cyclophilin-HIV capsid 2.4 1170 8 3 Gamble et al. (1996) 1efn Fyn SH3 domain-HIV Nef 2.5 1260 7 Lee et al. (1996) 1atn Actin-DNase I 2.8 1780 8 Kabsch et al. (1990) 2btf Actin-profilin…”