8GDV: Gag polyprotein
Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6. Determined by X-ray diffraction at 3.3 Å resolution. Released 13 Mar 2024.
- Method
- X-ray diffraction
- Resolution
- 3.3 Å
- Organisms
- Human immunodeficiency virus 1, Homo sapiens
- Chains
- 12
- Atoms
- 9,980
- Mol. weight
- 163.28 kDa
- Ligands
- IHP
- Released
- 13 Mar 2024
Explore 8GDV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8GDV contains 88 α-helices and 12 β-strands across 12 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.
Chain A: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 1 |
| β-strand | 11-12 | 2 | 1 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 179-184 | 6 | |
| α-helix | 185-189 | 5 | |
| α-helix | 190-192 | 3 | |
| α-helix | 196-202 | 7 | |
Chain B: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 2 |
| β-strand | 11-12 | 2 | 2 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 98-100 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 186-192 | 7 | |
| α-helix | 196-204 | 9 | |
| α-helix | 211-216 | 6 | |
Chain C: 12 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 3 |
| β-strand | 10-12 | 3 | 3 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-29 | 13 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-174 | 14 | |
| α-helix | 179-192 | 14 | |
| α-helix | 211-216 | 6 | |
Chain D: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 4 |
| β-strand | 10-12 | 3 | 4 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 186-192 | 7 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-216 | 6 | |
Chain E: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 5 |
| β-strand | 10-12 | 3 | 5 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 91-92 | 2 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-174 | 14 | |
| α-helix | 186-192 | 7 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-216 | 6 | |
Chain F: 13 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 6 |
| β-strand | 10-12 | 3 | 6 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-58 | 10 | |
| α-helix | 63-83 | 21 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 179-192 | 14 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chains M, N, P, Q and R: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 319-320 | 2 | |
Chain O: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 320 | 1 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Gag polyprotein | A, B, C, D, E, F | protein | 231 | Human immunodeficiency virus 1 | P12493 |
| Cleavage and polyadenylation specificity factor subunit 6 | M, N, O, P, Q, R | protein | 15 | Homo sapiens | Q16630 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8GDV_1 Gag polyprotein (chains A, B, C, D, E, F)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAIQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
Sequence of entity 2 (M, N, O, P, Q, R), FASTA
>8GDV_2 Cleavage and polyadenylation specificity factor subunit 6 (chains M, N, O, P, Q, R)
PVLFPGQPFGQPPLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| IHP | Inositol hexakisphosphate | C6 H18 O24 P6 | 2 |
Primary citation
Structural and mechanistic bases for resistance of the M66I capsid variant to lenacapavir. Briganti, L., Annamalai, A.S., Bester, S.M. et al. mBio (2025):e0361324-e0361324. DOI 10.1128/mbio.03613-24 · PubMed
Other PDB entries of the same protein (UniProt P12493), best resolution first:
- 8QUK 1.38 Å, Hexameric HIV-1 CA in complex with DDD00100439
- 8QUH 1.55 Å, Hexameric HIV-1 CA in complex with DDD00057456
- 8FIU 1.56 Å, Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile…
- 8QUB 1.63 Å, Hexameric HIV-1 CA in complex with DDD00074110
- 8QUJ 1.63 Å, Hexameric HIV-1 CA in complex with DDD00100452
- 8QUL 1.67 Å, Hexameric HIV-1 CA in complex with DDD00100555
- 8QUI 1.69 Å, Hexameric HIV-1 CA in complex with DDD00024969
- 5JPA 1.7 Å, Hexameric HIV-1 CA H12Y mutant
- 8QV9 1.76 Å, Hexameric HIV-1 CA in complex with DDD01829021
- 4U0C 1.77 Å, Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form
- 8VRP 1.8 Å, HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor
- 8QUY 1.88 Å, Hexameric HIV-1 CA in complex with DDD01728501
Browse structure collections
About this viewer
MolViewer shows 8GDV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.