7ZUD image
Entry Detail
PDB ID:
7ZUD
Keywords:
Title:
Crystal structure of HIV-1 capsid IP6-CPSF6 complex
Biological Source:
PDB Version:
Deposition Date:
2022-05-12
Release Date:
2022-07-27
Method Details:
Experimental Method:
Resolution:
2.93 Å
R-Value Free:
0.33
R-Value Work:
0.27
R-Value Observed:
0.27
Space Group:
P 6
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Capsid protein p24
Chain IDs:A
Chain Length:233
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Description:Cleavage and polyadenylation specificity factor subunit 6
Chain IDs:B (auth: M)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

Solution and solid-state NMR spectroscopy are highly complementary techniques for studying structure and dynamics in very high molecular weight systems. Here we have analysed the dynamics of HIV-1 capsid (CA) assemblies in presence of the cofactors IP6 and ATPγS and the host-factor CPSF6 using a combination of solution state and cross polarisation magic angle spinning (CP-MAS) solid-state NMR. In particular, dynamical effects on ns to µs and µs to ms timescales are observed revealing diverse motions in assembled CA. Using CP-MAS NMR, we exploited the sensitivity of the amide/Cα-Cβ backbone chemical shifts in DARR and NCA spectra to observe the plasticity of the HIV-1 CA tubular assemblies and also map the binding of cofactors and the dynamics of cofactor-CA complexes. In solution, we measured how the addition of host- and co-factors to CA -hexamers perturbed the chemical shifts and relaxation properties of CA-Ile and -Met methyl groups using transverse-relaxation-optimized NMR spectroscopy to exploit the sensitivity of methyl groups as probes in high-molecular weight proteins. These data show how dynamics of the CA protein assembly over a range of spatial and temporal scales play a critical role in CA function. Moreover, we show that binding of IP6, ATPγS and CPSF6 results in local chemical shift as well as dynamic changes for a significant, contiguous portion of CA, highlighting how allosteric pathways communicate ligand interactions between adjacent CA protomers.

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