7ZUD: HIV-1 capsid IP6-CPSF6 complex

Crystal structure of HIV-1 capsid IP6-CPSF6 complex. Determined by X-ray diffraction at 2.93 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.93 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 2
Atoms: 1,849
Mol. weight: 28.4 kDa
Ligands: IHP
Released: 27 Jul 2022

Explore 7ZUD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZUD contains 14 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: 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	49-58	10
α-helix	63-83	21
α-helix	91-92	2
α-helix	96-100	5
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-144	19
α-helix	161-174	14
α-helix	188-192	5
α-helix	196-205	10
α-helix	211-217	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein p24	A	protein	233	Human immunodeficiency virus 1	P12497
Cleavage and polyadenylation specificity factor subunit 6	M	protein	13	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ZUD_1 Capsid protein p24 (chains A)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLLE

Sequence of entity 2 (M), FASTA

>7ZUD_2 Cleavage and polyadenylation specificity factor subunit 6 (chains M)
PVLFPGQPFGQPP

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2

Primary citation

CP-MAS and Solution NMR Studies of Allosteric Communication in CA-assemblies of HIV-1. Nicastro, G., Lucci, M., Oregioni, A. et al. J Mol Biol (2022) 434:167691-167691. DOI 10.1016/j.jmb.2022.167691 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex

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