Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.8. Determined by X-ray diffraction at 1.9 Å resolution. Released 20 Jan 2016.
Explore 5FGC in 3D Show helices and sheets RCSB PDB PDBe
5FGC contains 17 α-helices and 47 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4 | 1 | 1 |
| β-strand | 5 | 1 | 2 |
| β-strand | 9-12 | 4 | 3 |
| α-helix | 17 | 1 | |
| β-strand | 18-23 | 6 | 2 |
| α-helix | 27-29 | 3 | |
| β-strand | 33-37 | 5 | 3 |
| β-strand | 44-47 | 4 | 3 |
| β-strand | 48 | 1 | 4 |
| β-strand | 52 | 1 | 4 |
| β-strand | 61-66 | 6 | 2 |
| β-strand | 69-74 | 6 | 2 |
| α-helix | 79-81 | 3 | |
| β-strand | 84-91 | 8 | 3 |
| β-strand | 95-98 | 4 | 3 |
| β-strand | 99 | 1 | 1 |
| β-strand | 102-106 | 5 | 3 |
| β-strand | 111 | 1 | 5 |
| α-helix | 112-113 | 2 | |
| β-strand | 114-118 | 5 | 6 |
| α-helix | 119-121 | 3 | |
| α-helix | 122-125 | 4 | |
| β-strand | 129-139 | 11 | 6 |
| β-strand | 140 | 1 | 5 |
| β-strand | 145-150 | 6 | 7 |
| β-strand | 153-155 | 3 | 7 |
| β-strand | 159-163 | 5 | 6 |
| α-helix | 164-167 | 4 | |
| β-strand | 173-182 | 10 | 6 |
| α-helix | 183-187 | 5 | |
| β-strand | 191-197 | 7 | 7 |
| β-strand | 205-210 | 6 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-8 | 6 | 8 |
| β-strand | 10-12 | 3 | 9 |
| β-strand | 18-25 | 8 | 8 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 9 |
| β-strand | 45-51 | 7 | 9 |
| β-strand | 58-60 | 3 | 9 |
| β-strand | 65 | 1 | 8 |
| β-strand | 68-73 | 6 | 8 |
| β-strand | 78-83 | 6 | 8 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-101 | 10 | 9 |
| β-strand | 112-117 | 6 | 9 |
| β-strand | 121-125 | 5 | 9 |
| α-helix | 128-130 | 3 | |
| β-strand | 131 | 1 | 10 |
| α-helix | 132-133 | 2 | |
| β-strand | 134-138 | 5 | 11 |
| β-strand | 149-159 | 11 | 11 |
| β-strand | 160 | 1 | 10 |
| β-strand | 165-168 | 4 | 12 |
| α-helix | 169-171 | 3 | |
| β-strand | 173 | 1 | 12 |
| β-strand | 178-179 | 2 | 11 |
| α-helix | 180-182 | 3 | |
| β-strand | 183-184 | 2 | 11 |
| β-strand | 190-199 | 10 | 11 |
| α-helix | 200-202 | 3 | |
| β-strand | 209-214 | 6 | 12 |
| α-helix | 215-217 | 3 | |
| β-strand | 219-224 | 6 | 12 |
| α-helix | 227-229 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Genome polyprotein | A | protein | 21 | Hepatitis C virus genotype 1a (isolate H) | P27958 (AlphaFold model) |
| Anti-HCV E2 Fab HC33.8 light chain | B | protein | 216 | Homo sapiens | |
| Anti-HCV E2 Fab HC33.8 heavy chain | E | protein | 269 | Homo sapiens |
>5FGC_1 Genome polyprotein (chains A) PGAKQNIQLINTNGSWHINST
>5FGC_2 Anti-HCV E2 Fab HC33.8 light chain (chains B) RSSYELTQPPSVSVSPGQAATITCSGDKLGDKYVSWYQQRPGQSPLLVVYQDNKRPSGIP ERISGSNSGNTATLTIRGTRAMDEADYYCQAWDSSTDVVFGGGTKLTVLRTVAAPSVFIF PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
>5FGC_3 Anti-HCV E2 Fab HC33.8 heavy chain (chains E) EVQLVESGGGLAQPGESLRLSCAASGFNFYTYAMTWVRQAPGKGLEWVSASSSTDGTTYY ADSVKGRFTISRDNSKNILYLQMNSLKAEDTATYYCARAVVFTDSSAYYYSKYFDYWSQG TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKLEDDDDKA GWSHPQFEKGGGSGGGSGGGSWSHPQFEK
Antibody Response to Hypervariable Region 1 Interferes with Broadly Neutralizing Antibodies to Hepatitis C Virus. Keck, Z.Y., Girard-Blanc, C., Wang, W. et al. J Virol (2016) 90:3112-3122. DOI 10.1128/JVI.02458-15 · PubMed
Other PDB entries of the same protein (UniProt P27958 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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