6AY9: Native full-length HIV-1 capsid protein

Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 12 Sept 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 2
Atoms: 1,835
Mol. weight: 27.82 kDa
Released: 12 Sept 2018

Explore 6AY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AY9 contains 15 α-helices and 2 β-strands across 1 chain. 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, 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	90-92	3
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	161-173	13
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-217	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 capsid protein	A	protein	231	Human immunodeficiency virus 1	P12493
Cleavage and polyadenylation specificity factor subunit 6	B	protein	12	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6AY9_1 HIV-1 capsid protein (chains A)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Sequence of entity 2 (B), FASTA

>6AY9_2 Cleavage and polyadenylation specificity factor subunit 6 (chains B)
PVLFPGQPFGQP

Primary citation

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Gres, A.T., Kirby, K.A., McFadden, W.M. et al. Nat Commun (2023) 14:5614-5614. DOI 10.1038/s41467-023-41197-7 · 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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