Structural comparison of 05.GC.w2.3C10-H1, 05.GC.w13.01-H1, 05.GC.w13.02-H1, and 05.GC.w13.02-H5. Related to Figs. 4 and 5. (A) Overall binding model of each HA-Fab complex from their x-ray (panel 1, 3, 4, and 5) and cryo-EM (panel 2) structures. The Fabs are shown in surface representation. HA is represented as a trimer in backbone cartoon, with one HA monomer highlighted to illustrate the interaction between HA and Fab. (B and C) Local resolution (B) and Fourier Shell Correlation (C) of the cryo-EM structure of 3C10 Fab in complex with A/Solomon Islands/3/2006 (SI06) H1N1 HA. (D) The CDR loops of each Fab in contact with HA are shown with the loops as cartoons. (E) Hydrophobic residues involved in the contact between Fabs and HA are represented as sticks. Three hydrophobic areas in the stem region in H1 HA are circled and the underlying surface is represented in a green hydrophobicity gradient calculated by Color (https://pymolwiki.org/index.php/Color). (F) Critical hydrophobic residues in the heavy chain involved in interaction between Fab and HA are shown in side-chain sticks. (G) Superimposition of each Fab-HA complex and Apo-H1. The Thr61 side chain is illustrated as an indicator of the relative disposition of the interhelical loop among these structures. Distances in Angstroms were measured from T61 in 05.GC.w13.02-H1 to Apo-H1, and between 05.GC.w13.02-H1 and 05.GC.w13.02-H5. 05.GC.w2.3C10 is in yellow, 05.GC.w13.01-H1 in sand, 05.GC.w13.02-H1 in teal, 05.GC.w13.02-H5 in orange, and Apo-H1 in light blue (PDB: 4M4Y). The HA is shown in a backbone cartoon. (H) The extent of the upper pocket in each complex is measured from T290 (S290 in 05.GC.w13.02-H5) in the 290-loop to T61 in the interhelical loop after superimposition of HA1 and HA2 from each complex and Apo-H1. (I) The flexible 290-loop, 300-loop, and interhelical loop in the upper pocket in the stem region are highlighted in red. (J) 05.GC.w2.3C10-H1_SI06 complex determined by cryo-EM is shown in green. The extent of the upper pocket is measured from the distance between S290 and T61 in the 290-loop and interhelical loop, respectively (left). Superimposition of 05.GC.w2.3C10-H1_SI06 complex onto the 05.GC.w2.3C10-H1 (right). (K) Binding mode of Fab HCDR1, HCDR2, and HCDR3 loops with H1 HA. Residues involved in hydrophobic interactions are in red with black labels for HA residues and CDR loops. (L) Binding orientation of the Fab VH domain to HA and location of residues 98 in 05.GC.w2.3C10, 05.GC.w13.01, and 05.GC.w13.02 compared to CR9114. (M) Binding kinetics of 05.GC.w13.02 with alanine substitutions in critical contact positions using BLI. Black lines illustrate the response curves representing a 1:1 binding model of Fab with CA04 H1 HA.
Figure S4.

Structural comparison of 05.GC.w2.3C10-H1, 05.GC.w13.01-H1, 05.GC.w13.02-H1, and 05.GC.w13.02-H5. Related to Figs. 4 and 5. (A) Overall binding model of each HA-Fab complex from their x-ray (panel 1, 3, 4, and 5) and cryo-EM (panel 2) structures. The Fabs are shown in surface representation. HA is represented as a trimer in backbone cartoon, with one HA monomer highlighted to illustrate the interaction between HA and Fab. (B and C) Local resolution (B) and Fourier Shell Correlation (C) of the cryo-EM structure of 3C10 Fab in complex with A/Solomon Islands/3/2006 (SI06) H1N1 HA. (D) The CDR loops of each Fab in contact with HA are shown with the loops as cartoons. (E) Hydrophobic residues involved in the contact between Fabs and HA are represented as sticks. Three hydrophobic areas in the stem region in H1 HA are circled and the underlying surface is represented in a green hydrophobicity gradient calculated by Color (https://pymolwiki.org/index.php/Color). (F) Critical hydrophobic residues in the heavy chain involved in interaction between Fab and HA are shown in side-chain sticks. (G) Superimposition of each Fab-HA complex and Apo-H1. The Thr61 side chain is illustrated as an indicator of the relative disposition of the interhelical loop among these structures. Distances in Angstroms were measured from T61 in 05.GC.w13.02-H1 to Apo-H1, and between 05.GC.w13.02-H1 and 05.GC.w13.02-H5. 05.GC.w2.3C10 is in yellow, 05.GC.w13.01-H1 in sand, 05.GC.w13.02-H1 in teal, 05.GC.w13.02-H5 in orange, and Apo-H1 in light blue (PDB: 4M4Y). The HA is shown in a backbone cartoon. (H) The extent of the upper pocket in each complex is measured from T290 (S290 in 05.GC.w13.02-H5) in the 290-loop to T61 in the interhelical loop after superimposition of HA1 and HA2 from each complex and Apo-H1. (I) The flexible 290-loop, 300-loop, and interhelical loop in the upper pocket in the stem region are highlighted in red. (J) 05.GC.w2.3C10-H1_SI06 complex determined by cryo-EM is shown in green. The extent of the upper pocket is measured from the distance between S290 and T61 in the 290-loop and interhelical loop, respectively (left). Superimposition of 05.GC.w2.3C10-H1_SI06 complex onto the 05.GC.w2.3C10-H1 (right). (K) Binding mode of Fab HCDR1, HCDR2, and HCDR3 loops with H1 HA. Residues involved in hydrophobic interactions are in red with black labels for HA residues and CDR loops. (L) Binding orientation of the Fab VH domain to HA and location of residues 98 in 05.GC.w2.3C10, 05.GC.w13.01, and 05.GC.w13.02 compared to CR9114. (M) Binding kinetics of 05.GC.w13.02 with alanine substitutions in critical contact positions using BLI. Black lines illustrate the response curves representing a 1:1 binding model of Fab with CA04 H1 HA.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal