Chapter 3 : Antibody Structure

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Currently, well over 1,000 antibody Fab or Fab variable (Fv) structures have been determined and deposited in the Protein Data Bank (www.rcsb.org). Many of these antibodies target proteins found on or secreted by infectious agents, such as viruses or bacteria. At first glance, one antibody Fab fragment may look just like another, but closer inspection shows that these workhorses of the adaptive immune system can capitalize on novel structural features to tailor their binding sites to accommodate targets of diverse shapes, sizes, and properties. Recent crystallographic and electron microscopy studies of human antibodies against human immunodeficiency virus type 1 (HIV-1) and influenza viruses have revealed some unusual structural features and modes of antigen recognition that enable these antibodies to effectively and broadly neutralize their rapidly evolving targets. We will focus here on immunoglobulin G (IgG) antibodies, as these are the best characterized from a structural perspective.

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Figure 1

Extremely long CDR H3 loops in human anti-HIV-1 antibodies targeting the V1/V2 region of gp120 in the Env trimer. Fab PG16 (left, PDB 3mug) has a large (28/30 residue), structured “hammerhead” CDR H3 (red) with posttranslational modifications of one sulfated tyrosine and one N-linked glycan. PG9 (middle, PDB 3u4e) in complex with the V1/V2 domain (yellow) from HIV-1 gp120 (CAP45 isolate) uses its large CDR H3 to bisect two glycans (shown in yellow ball-and-stick representation) and form a parallel β-sheet interaction with one strand from V1/V2. PG9 has two sulfated tyrosine residues at its tip. Fab PGT145 (right, PDB 3u1s) has the longest CDR H3 (31/33 residues) yet seen in human antibodies. This CDR also has two sulfated tyrosine residues at its tip. For the Cα trace of both Fabs, the CDR loops are colored orange (L1), magenta (L2), green (L3), blue (H1), pink (H2), and red (H3), with light chains in light gray and heavy chains in dark gray. All figures were made with MOLSCRIPT ( ) and rendered with Raster3D ( ).

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Image of Figure 2
Figure 2

Broadly neutralizing Fab CR6261 (left) uses only its heavy chain (dark gray, with blue, pink, and red CDR loops) to recognize the stem region of a hemagglutinin trimer. Fab C05 (right) binds to a conserved region near the receptor binding site, using mainly its large CDR H3 (red), with minor contact from CDR H1 (blue).

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Image of Figure 3
Figure 3

Self-carbohydrate recognition by HIV-1 antibodies. (Left) Dimeric, domain-swapped 2G12 binds the D1 arms of GlcNAcMan (yellow) via two closely spaced primary combining sites. A third potential binding site, located between the closely spaced V and V′ domains, binds symmetry-related sugars (orange). (Middle and right) PGT128 also binds to two sugar moieties and inserts its CDR H3 (red) and long H2 (magenta) between two high-mannose sugars to contact the protein surface. The Fab-antigen complex is shown from two different sides to illustrate the interaction. 2G12, PGT128, and PG9 ( Fig. 1 ) bind two high-mannose sugars, either with two separate binding sites, as in 2G12, or by wedging long CDR loops between two carbohydrates, as in PGT128 and PG9 recognition.

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Figure 4

Diversity in the shape of antibody combining sites. Fab domain swapping and extremely long CDR H3 loops result in unusually shaped paratopes. (Top) Fv molecular surfaces are shown in gray, with paratopes (if known) colored in magenta and antigens shown in yellow. Classic antibody binding sites are usually pockets for small haptens (DB3, progesterone), grooves for peptides (B13I2, myohemerythrin peptide; 17/9, influenza peptide), or flat, undulating surfaces for proteins (HyHEL-10, lysozyme; HyHEL-5, lysozyme). (Bottom) In contrast, domain-swapped 2G12 has created a paratope consisting of 4 different binding pockets, and PGT128 and PG9 have protruding, convex paratopes that can be inserted between two large carbohydrate moieties. A structure of PGT145 with its antigen has not yet been determined, but its very long CDR H3 can be clearly visualized.

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Figure 5

Unusual insertions in CDRs H1 and H2 from Fabs C05 (red), 2D1 (yellow), and PGT128 (blue). (Left) In these H1 CDRs, the colored areas cover residues H26 to H35b. C05 has an unusually long 5-residue insertion in H1, while PGT128 and 2D1 have more common 2-residue insertions in H1. The 2D1 H1 CDR has shifted away its canonical conformation due to a clash with its long H2 loop. (Right) H2 CDRs from the same Fabs, with the same coloring from positions H51 to H57. C05 has a normal H2 CDR with a 1-residue insertion after residue 52. PGT128 has a very rare 6-residue insertion in this CDR, which is reflected in its unusually long H2 CDR loop. 2D1 has a 3-residue insertion in the CDR that extends the physical CDR length by 1 residue, but the other inserted residues are accommodated in the loop around H63–H64 that faces the C1 domain.

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013
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Generic image for table

CDR lengths and posttranslational modifications of unusual human antibodies

Citation: Stanfield R, Wilson I. 2015. Antibody Structure, p 49-62. In Crowe J, Boraschi D, Rappuoli R (ed), Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.AID-0012-2013

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