Volume 11, Issue 7, Pages (July 2003)

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Volume 11, Issue 7, Pages 875-885 (July 2003) The Crystal Structure of Human Angiogenin in Complex with an Antitumor Neutralizing Antibody Gayatri B Chavali, Anastassios C Papageorgiou, Karen A Olson, James W Fett, Guo-fu Hu, Robert Shapiro, K.Ravi Acharya Structure Volume 11, Issue 7, Pages 875-885 (July 2003) DOI: 10.1016/S0969-2126(03)00131-X

Figure 1 Structure of the Complex Formed between Human ANG and Fab 26-2F The L and H chains of the Fab molecule are in magenta and blue, respectively, except for their CDRs (L1–L3 and H1–H3), which are in gold and cyan, respectively. ANG, green. Sulfate ions (yellow bonds) and glycerol molecules (green bonds) are also shown. The figure was generated with MOLSCRIPT (Kraulis, 1991). Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)

Figure 2 Amino Acid Sequences of Fab 26-2F and Human ANG The antibody V region sequences are those deduced from the DNA sequence (Piccoli et al., 1998); GenBank accession numbers are AF039414 (VL) and AF039415 (VH). Residue numbering is that of Chothia and Lesk (1987). Residues that are highly conserved in this IgG subclass are shown in bold italic type. The six CDR loops as defined by the antibody modeling programs AbM (Oxford Molecular) and WAM (Whitelegg and Rees, 2000; http://antibody.bath.ac.uk/WAMpredict.html) are underlined; these definitions differ from those of Chothia and coworkers (Chothia and Lesk, 1987; Chothia et al. 1989; Al-Lazikani et al., 1997) only for CDRs H1 and H2. The DNA sequences for the CL and CH regions have not been determined; the amino acid sequences shown are those from MOPC 41 and MOPC 21, respectively (Kabat et al., 1991), except for three residues (L146, L165, and H89) where the crystal structure clearly reveals differences. The ANG sequence is from Strydom et al. (1985). Residues involved in intermolecular contacts are highlighted in magenta. Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)

Figure 3 Stereo View of the Superposed Cα Backbones of the Fab Molecule from the ANG-Fab 26-2F Complex (Magenta) and Fab D44.1 (Protein Data Bank Code 1MLB; Blue) The locations of the CDRs (L1–L3 and H1–H3) are indicated. Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)

Figure 4 Structural Details of the Interactions at the ANG/Fab 26-2F Interface (A) The interface region of the complex of Fab 26-2F and ANG, showing the van der Waals surface for the Fab, stick representations (in standard colors) for ANG residues that contact the antibody, and a trace for the ANG backbone (magenta). The CDRs of the Fab, green. The figure was generated with the program DINO (A. Philippsen; http://cobra.mih.unibas.ch/dino/). (B) Stereo view of the details of the hydrogen bonding contacts in the complex. Hydrogen bonding residues on ANG and the Fab are shown as stick representations, along with their respective backbone traces (magenta and green, respectively). CDRs are labeled in bold type. Potential hydrogen bonds are drawn as broken lines. Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)

Figure 5 Superposition of the Cα Atoms of Free ANG (Protein Data Bank Code 1B1I; Orange) and ANG from the Fab 26-2F Complex (Dark Green) The two loops that contact the Fab are indicated. The region containing cell binding site residues 60–68 is circled and shown below with a portion of the Fo − Fc electron density map clearly showing the deviation in the conformation of this region in Fab-bound ANG. The map is contoured at 3.0 σ. The figure was created with BOBSCRIPT (Esnouf, 1997) and RASTER 3D (Merritt and Bacon, 1997). Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)

Figure 6 Effect of mAb 26-2F on the Binding of ANG to ANG Binding Protein (ANGBP) 125I-ANG was incubated for 30 min in the presence or absence of a 10-fold molar excess of mAb prior to addition of ANGBP or PBS. After 10 min of further incubation, samples were subjected to crosslinking with carbodiimide and then analyzed by SDS-PAGE and autoradiography. Lane 1, ANG alone; lane 2, ANG plus ANGBP; lanes 3, 5, and 7, ANG plus mAb 26-2F, 36u, or 32-B5, respectively; lanes 4, 6, and 8, ANG plus mAb (26-2F, 36u, and 32-B5, respectively) and ANGBP; lane 9, molecular weight standards. The extent of the reduction in crosslinking of ANG to ANGBP due to preincubation with mAB 26-2F (lane 4 versus lane 2) in this experiment, as determined by densitometry, is 70%. Structure 2003 11, 875-885DOI: (10.1016/S0969-2126(03)00131-X)