4U0D: Hexameric HIV-1 CA

Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form. Determined by X-ray diffraction at 3.0 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B, Homo sapiens
Chains: 18
Atoms: 19,269
Mol. weight: 315.7 kDa
Released: 12 Nov 2014

Explore 4U0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U0D contains 167 α-helices and 32 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: 15 helices, 3 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	85-87	3
α-helix	94-95	2
β-strand	96	1	2
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	161-175	15
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-217	7

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	3
β-strand	11-12	2	3
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	101-105	5
α-helix	111-118	8
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

Chain C: 16 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	4
β-strand	11-12	2	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	90	1
β-strand	91	1	5
α-helix	92	1
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-176	16
α-helix	184-192	9
α-helix	196-205	10
α-helix	211-217	7

Chain D: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	6
β-strand	11-12	2	6
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	7
α-helix	92	1
α-helix	97-100	4
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	161-175	15
α-helix	185-192	8
α-helix	196-205	10
α-helix	211-217	7

Chains E, I and L: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
β-strand	11-12	2	8
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	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	161-174	14
α-helix	189-192	4
α-helix	196-205	10
α-helix	211-217	7

Chain F: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
β-strand	11-12	2	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
β-strand	96	1	10
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	161-175	15
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-217	7

Chain G: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	11
β-strand	11-12	2	11
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	7
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	179-189	11
α-helix	196-205	10
α-helix	211-217	7

Chain H: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	12
β-strand	11-12	2	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	95	1
β-strand	96	1	5
α-helix	97-100	4
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	161-174	14
α-helix	189-192	4
α-helix	196-203	8
α-helix	211-217	7

1 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
Gag polyprotein	A, B, C, D, E, F, G, H, I, J, K, L	protein	231	Human immunodeficiency virus type 1 group M subtype B	P12493
Nuclear pore complex protein Nup153	M, N, O, P, Q, R	protein	17	Homo sapiens	P49790 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>4U0D_1 Gag polyprotein (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), FASTA

>4U0D_2 Nuclear pore complex protein Nup153 (chains M, N, O, P, Q, R)
TNNSPSGVFTFGANSST

Primary citation

Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly. Price, A.J., Jacques, D.A., McEwan, W.A. et al. PLoS Pathog (2014) 10:e1004459-e1004459. DOI 10.1371/journal.ppat.1004459 · 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 4U0D 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.