Table 2.
Ligand conformation and HAs co-complexed to α2-6 and α2-3 oligosaccharides (resolution ≤ 2.5 Å)
| PDB ID, ligand | α2-6 | PDB ID, ligand | α2-3 | HA virus strain | Amino acids at 190,193,222, 225, 226, 227, 228 |
|---|---|---|---|---|---|
| ψa | φb | ||||
| H1N1 | |||||
| 1RVT, LSTc | anti | 1RV0, LSTa | –c | A/Swine/Iowa/15/1930 | D,S,K,G,Q,A,G |
| 1RVZ, LSTc | anti | 1RVX, LSTa | anti | A/Puerto Rico/8/1934 | E,D,K,D,Q,A,G |
| 3UBE, LSTc | anti | 3UBJ, LSTa | anti | A/California/04/2009 | D,S,K,D,Q,E,G |
| 3UBN, 6′SLN | anti | 3UBQ, 3′SLN | anti | A/California/04/2009 | D,S,K,D,Q,E,G |
| 3HTQd, LSTc | anti | 3HTPd, LSTa | anti | A/Wild Duck/JX/12416/2005 | E,T,K,G,Q,A,G |
| H2N2 | |||||
| 2WR1, LSTc | anti | 2WR2, LSTa | anti | A/Chicken/New York/29878/91 | E,T,K,G,Q,G,G |
| 2WR4, LSTc | anti | 2WR3, LSTa | anti | A/Duck/Ontario/1977 | E,T,K,G,Q,G,G |
| 2WR7, LSTc | anti | – | A/Singapore/1/57 | E,T,K,G,L,G,S | |
| H3N2 | |||||
| 2YP3, 6′SLN | anti | 2YP5, 3′SLN | –c | A/Finland/486/2004 | D,S,R,D,I,P,S |
| 2YP4, LSTc | anti | A/Finland/486/2004 | D,S,R,D,I,P,S | ||
| 2YP8, 6′SLN | –c | 2YP9, 3′SLN | –c | A/Hong Kong/4443/2005 | D,F,R,N,I,P,S |
| 2YPGd, LSTc | anti | A/Aichi/2/1968-X31 | E,S,W,G,L,S,S | ||
| H3N8 | |||||
| 4WA2, 3′SLN | anti | A/harbor seal/Massachusetts/1/2011 | E,N,L,G,Q,S,G | ||
| H5N1 | |||||
| 1JSO, LSTc | –c | 1JSN, LSTa | anti | A/Duck/Singapore/3/1997 | E,K,K,G,Q,S,G |
| 4BGX, 6′SLN | eclipsedb | 4BGYd, 3′SLN | anti | A/Vietnam/1194/2004 | E,K,K,G,Q,S,G |
| 4BH0, 6′SLN | eclipsed | 4BH1, 3′SLN | anti | A/Turkey/Turkey/1/2005 | E,R,K,G,Q,S,G |
| 4BH3, 6′SLN | anti | 4BH4, 3′SLN | –gaucheb | A/Vietnam/1203/2004 (N158D,N224Q,Q226L,T318I) | E,K,K,G,L,S,G |
| 4KDO, LSTc | anti | 4KDN, LSTa | –c | A/Vietnam/1203/2004 (N158D/N224K/Q226L/T318I) | E,K,K,G,L,S,G |
| 4CQR, 6′SLN | eclipsed | 4CQQd, 3′SLN | –gauche | A/Vietnam/1194/2004 (S227N,Q196R) | E,K,K,G,Q,R,G |
| 4CQU, 6′SLN | eclipsed | 5AJM, 3′SLN | –gauche | A/Vietnam/1194/2004 (N186K) | E,K,K,G,Q,S,G |
| 4CQY, LSTa | anti | A/turkey/Turkey/1/2005 (Δ133/I155T) | E,R,K,G,Q,S,G | ||
| 4CQX, 6′SLN | eclipsed | 4CQW, 3′SLN | anti | A/turkey/Turkey/1/2005 (Δ133/I155T) | E,R,K,G,Q,S,G |
| H6N1 | |||||
| 5BR6a, LSTc | anti | 5BR3d, LSTa | –gauche | A/Taiwan/2/2013 | V,N,A,G,Q,R,S |
| 4XKF, LSTa | –gauche | A/Taiwan/2/2013 | V,N,A,G,Q,R,S | ||
| 4XKG, 6′SLN | eclipsed | 4XKE, 3′SLN | –gauche | A/Taiwan/2/2013 | V,N,A,G,Q,R,S |
| H7N3 | |||||
| 4BSH, 6′SLN | eclipsed | 4BSI, 3′SLNd | anti | A/Turkey/Italy/214845/2002 | E,K,Q,G,Q,S,G |
| H7N9 | |||||
| 4BSB, LSTc | anti | A/Anhui/1/2013 (L20,T135) | E,K,Q,G,L,S,G | ||
| 4BSCd, 6′SLN | anti | 4BSD, 3′SLN | –gauche | A/Anhui/1/2013 (L20,T135) | E,K,Q,G,L,S,G |
| 4BSEd, LSTc | anti | A/Anhui/1/2013 (V20,A135) | E,K,Q,G,L,S,G | ||
| 4LKKa, 6′SLNLN | anti | 4LKJd, 3′SLNLN | anti | A/Anhui/1/2013 (L226Q) | E,K,Q,G,Q,S,G |
| 4N62, 3′SL(6S)N | +gauchee | A/Shanghai/2/2013 (L226) | E,K,Q,G,L,S,G | ||
| H9N2 | |||||
| 1JSI, LSTc | anti | 1JSH, LSTa | –gauche | A/Swine/Hong Kong/9/1998 | V,N,L,G,L,H,G |
| H10N2 | |||||
| 4CYZ, LSTa | anti | A/mallard/Sweden/51/2002 | E,D,Q,G,Q,S,G | ||
| H10N8 | |||||
| 4D00, 6′SLN | anti and eclipsedf | A/Jiangxi-Donghu/346/2013 | E,D,Q,G,Q,S,G | ||
For α2-6 linkages, ψ (C2′–O6–C6–C5) adopts either an anti (188° ± 23) or eclipsed (113° ± 7) conformation. The remaining glycosidic angles adopt a single conformation characterized by average φ (C1′–C2′–O6–C6) = −55° ± 11 (–gauche, a.k.a. ‘cis’) and average ω (O6–C6–C5–O5) = 63° ± 17, with the exceptions of 5BR6, where φ = 201°, and ω = −41°, 4LKK, where ω = 157°.
For α2-3 linkages, φ (C1′–C2′–O3–C3) adopts either an anti (185° ± 10, a.k.a. ‘trans’) or –gauche (−57° ± 8, a.k.a. ‘cis’) conformation. The ψ (C2–O3–C3–C4) glycosidic angle adopt a single conformation average ψ = 100° ± 11.
Only the Sia residue is resolved.
Resolution > 2.5 Å.
Distorted Sia-1 and GlcNAc-3 rings, high B-factors.
Eclipsed in chain E.