4WYM: HIV-1 capsid recognition by CPSF6
Structural basis of HIV-1 capsid recognition by CPSF6. Determined by X-ray diffraction at 2.6 Å resolution. Released 17 Dec 2014.
- Method
- X-ray diffraction
- Resolution
- 2.6 Å
- Organisms
- Human immunodeficiency virus type 1 group M subtype B, Homo sapiens
- Chains
- 23
- Atoms
- 20,913
- Mol. weight
- 324.33 kDa
- Released
- 17 Dec 2014
Explore 4WYM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4WYM contains 199 α-helices and 36 β-strands across 21 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: 17 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| β-strand | 10-12 | 3 | 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 | 85-88 | 4 | |
| α-helix | 90 | 1 | |
| β-strand | 91 | 1 | 2 |
| α-helix | 92 | 1 | |
| α-helix | 96-99 | 4 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 185-192 | 8 | |
| α-helix | 196-201 | 6 | |
| α-helix | 211-217 | 7 | |
Chain B: 15 helices, 3 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 | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-82 | 20 | |
| α-helix | 95 | 1 | |
| β-strand | 96 | 1 | 4 |
| 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 | 180-192 | 13 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain C: 17 helices, 3 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 | 95 | 1 | |
| β-strand | 96 | 1 | 6 |
| 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 | 161-175 | 15 | |
| α-helix | 179-184 | 6 | |
| α-helix | 185-189 | 5 | |
| α-helix | 190-192 | 3 | |
| α-helix | 196-203 | 8 | |
| α-helix | 211-217 | 7 | |
Chain D: 15 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 7 |
| β-strand | 10-12 | 3 | 7 |
| 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 | 95 | 1 | |
| β-strand | 96 | 1 | 8 |
| 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 | 161-175 | 15 | |
| α-helix | 187-190 | 4 | |
| α-helix | 196-202 | 7 | |
| α-helix | 211-217 | 7 | |
Chain E: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 9 |
| β-strand | 10-12 | 3 | 9 |
| 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 | 179-188 | 10 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain F: 16 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 10 |
| β-strand | 10-12 | 3 | 10 |
| 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 | 90 | 1 | |
| β-strand | 91 | 1 | 11 |
| α-helix | 92 | 1 | |
| α-helix | 96-99 | 4 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-144 | 19 | |
| 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 | |
Chain G: 17 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 12 |
| β-strand | 10-12 | 3 | 12 |
| 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 | 90 | 1 | |
| β-strand | 91 | 1 | 8 |
| α-helix | 92 | 1 | |
| 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 | 154-156 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 187-192 | 6 | |
| α-helix | 196-203 | 8 | |
| α-helix | 211-217 | 7 | |
Chain H: 15 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 13 |
| β-strand | 10-12 | 3 | 13 |
| 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 | 90 | 1 | |
| β-strand | 91 | 1 | 6 |
| α-helix | 92 | 1 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-144 | 19 | |
| α-helix | 161-174 | 14 | |
| α-helix | 188-192 | 5 | |
| α-helix | 196-202 | 7 | |
| α-helix | 211-215 | 5 | |
6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Capsid protein p24 | A, B, C, D, E, F, G, H, I, J, K, L | protein | 231 | Human immunodeficiency virus type 1 group M subtype B | P12493 |
| Isoform 2 of cleavage and polyadenylation specificity factor subunit 6 | M, N, O, P, Q, R, S, T, U, V, W | protein | 17 | Homo sapiens | Q16630 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA
>4WYM_1 Capsid protein p24 (chains A, B, C, D, E, F, G, H, I, J, K, L)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
Sequence of entity 2 (M, N, O, P, Q, R, S, T, U, V, W), FASTA
>4WYM_2 ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 (chains M, N, O, P, Q, R, S, T, U, V, W)
GTPVLFPGQPFGQPPLG
Primary citation
Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Bhattacharya, A., Alam, S.L., Fricke, T. et al. Proc Natl Acad Sci U S A (2014) 111:18625-18630. DOI 10.1073/pnas.1419945112 · 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
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