7ZUD

Crystal structure of HIV-1 capsid IP6-CPSF6 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

CP-MAS and Solution NMR Studies of Allosteric Communication in CA-assemblies of HIV-1.

Nicastro, G.Lucci, M.Oregioni, A.Kelly, G.Frenkiel, T.A.Taylor, I.A.

(2022) J Mol Biol 434: 167691-167691

  • DOI: https://doi.org/10.1016/j.jmb.2022.167691
  • Primary Citation of Related Structures:  
    7ZUD

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein p24233Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 6B [auth M]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16630 (Homo sapiens)
Explore Q16630 
Go to UniProtKB:  Q16630
GTEx:  ENSG00000111605 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16630
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.741α = 90
b = 90.741β = 90
c = 56.588γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
STARANISOdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001178
Wellcome TrustUnited Kingdom108014/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description