8CL1: HIV-1 mature capsid hexamer from CA-IP6 CLPs

HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to CPSF6 peptide. Determined by electron microscopy at 3.35 Å resolution. Released 26 Apr 2023.

Method: Electron microscopy
Resolution: 3.35 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 2
Atoms: 1,749
Mol. weight: 27.31 kDa
Released: 26 Apr 2023

Explore 8CL1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CL1 contains 16 α-helices and 2 β-strands across 2 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	97-100	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-218	8

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	320	1
α-helix	323-325	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag polyprotein	A	protein	232	Human immunodeficiency virus 1	P12493
Cleavage and polyadenylation specificity factor subunit 6	B	protein	15	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8CL1_1 Gag polyprotein (chains A)
MPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTV
GGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMT
HNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQ
EVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Sequence of entity 2 (B), FASTA

>8CL1_2 Cleavage and polyadenylation specificity factor subunit 6 (chains B)
PVLFPGQPFGQPPLG

Primary citation

Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding. Stacey, J.C.V., Tan, A., Lu, J.M. et al. Proc Natl Acad Sci U S A (2023) 120:e2220557120-e2220557120. DOI 10.1073/pnas.2220557120 · 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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