8CL0: Gag polyprotein

HIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6 CLPs bound to Nup153 peptide. Determined by electron microscopy at 3.12 Å resolution. Released 26 Apr 2023.

Method: Electron microscopy
Resolution: 3.12 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 10,387
Mol. weight: 164.7 kDa
Released: 26 Apr 2023

Explore 8CL0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CL0 contains 97 α-helices and 12 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	2-4	3	1
β-strand	10-12	3	1
α-helix	13-16	4
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-58	10
α-helix	63-83	21
α-helix	96-100	5
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
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	211-217	7

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-12	3	2
α-helix	13-16	4
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-58	10
α-helix	63-83	21
α-helix	98-100	3
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
α-helix	161-175	15
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-203	8
α-helix	211-217	7

Chain C: 17 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	36-44	9
α-helix	49-58	10
α-helix	63-83	21
α-helix	85-87	3
α-helix	97-100	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
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	196-204	9
α-helix	211-218	8

Chain D: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	4
β-strand	10-12	3	4
α-helix	13-16	4
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-58	10
α-helix	63-83	21
α-helix	96-100	5
α-helix	101-104	4
α-helix	111-119	9
α-helix	126-144	19
α-helix	150-152	3
α-helix	155-156	2
α-helix	161-175	15
α-helix	179-192	14
α-helix	196-204	9
α-helix	211-218	8

Chain E: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	5
β-strand	10-12	3	5
α-helix	13-16	4
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-58	10
α-helix	63-83	21
α-helix	98-100	3
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
α-helix	150-152	3
α-helix	155-156	2
α-helix	161-175	15
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-204	9
α-helix	206	1
α-helix	211-217	7

Chain F: 16 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	49-58	10
α-helix	63-83	21
α-helix	96-100	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	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-203	8
α-helix	211-218	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag polyprotein	A, B, C, D, E, F	protein	232	Human immunodeficiency virus 1	P12493
Nuclear pore complex protein Nup153	G, H, I, J, K, L	protein	17	Homo sapiens	P49790 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>8CL0_1 Gag polyprotein (chains A, B, C, D, E, F)
MPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTV
GGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMT
HNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQ
EVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>8CL0_2 Nuclear pore complex protein Nup153 (chains G, H, I, J, K, L)
TNNSPSGVFTFGANSST

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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