5TSX: HIV-1 CA protein

HIV-1 CA hexamer with NUP153 peptide - P1 crystal form. Determined by X-ray diffraction at 1.9 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B (isolate NY5), Homo sapiens
Chains: 18
Atoms: 22,652
Mol. weight: 320.14 kDa
Ligands: FLU
Released: 8 Nov 2017

Explore 5TSX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TSX contains 176 α-helices and 24 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	2-4	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	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	161-176	16
α-helix	184-192	9
α-helix	196-205	10
α-helix	211-217	7

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-12	3	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	101-104	4
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 C: 16 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	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	95-99	5
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	179-185	7
α-helix	186-190	5
α-helix	191-192	2
α-helix	196-205	10
α-helix	211-217	7

Chains D and K: 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	96-99	4
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

Chain E: 16 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	97-99	3
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	179-185	7
α-helix	186-190	5
α-helix	191-192	2
α-helix	196-205	10
α-helix	211-217	7

Chain F: 14 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	49-57	9
α-helix	63-83	21
α-helix	96-99	4
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	179-192	14
α-helix	196-205	10
α-helix	211-217	7

Chain G: 14 helices, 2 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	97-99	3
α-helix	101-104	4
α-helix	111-119	9
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 H: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	8
β-strand	10-12	3	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	85-88	4
α-helix	90-92	3
α-helix	96-99	4
α-helix	101-104	4
α-helix	111-119	9
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-176	16
α-helix	185-192	8
α-helix	196-205	10
α-helix	211-217	7

3 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
HIV-1 CA protein	A, B, C, D, E, F, G, H, I, J, K, L	protein	231	Human immunodeficiency virus type 1 group M subtype B (isolate NY5)	P12493
Nuclear pore complex protein Nup153	M, N, O, P, R, T	protein	23	Homo sapiens	P49790 (AlphaFold model)

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

>5TSX_1 HIV-1 CA protein (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, R, T), FASTA

>5TSX_2 Nuclear pore complex protein Nup153 (chains M, N, O, P, R, T)
TNNSPSGVFTFGANSSTPAASAQ

Ligands and cofactors

ID	Name	Formula	Copies
FLU	2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid	C20 H12 O5	4

Primary citation

HIV-1 CA hexamer with NUP153 peptide - P1 crystal form. Skorupka, K., Zadrozny, K., Ganser-Pornillos, B.K. et al. To be published.

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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