8EJL: HIV-1 capsid declination

Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide. Determined by electron microscopy at 3.9 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 4,431
Mol. weight: 105.94 kDa
Released: 15 Feb 2023

Explore 8EJL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EJL contains 48 α-helices and 4 β-strands across 6 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	2
β-strand	12	1	2
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-56	8
α-helix	59-61	3
α-helix	63-80	18
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	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-216	6

Chain L: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	12	1	1
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	123-124	2
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Chain M: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-29	13
α-helix	36-42	7
α-helix	49-57	9
α-helix	63-83	21
α-helix	111-119	9
α-helix	123	1
α-helix	126-144	19

Chain N: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Chains Y and Z: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	320	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 capsid protein	A, L, M, N	protein	231	Human immunodeficiency virus 1	P12493
Cleavage and polyadenylation specificity factor subunit 6	Y, Z	protein	17	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A, L, M, N), FASTA

>8EJL_1 HIV-1 capsid protein (chains A, L, M, N)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Sequence of entity 2 (Y, Z), FASTA

>8EJL_2 Cleavage and polyadenylation specificity factor subunit 6 (chains Y, Z)
GTPVLFPGQPFGQPPLG

Primary citation

A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Schirra, R.T., Dos Santos, N.F.B., Zadrozny, K.K. et al. Nat Struct Mol Biol (2023) 30:383-390. DOI 10.1038/s41594-022-00913-5 · 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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