Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 118, Issue 3, Year 2021
Publish date	Jan 19, 2021
Authors	Aaron Tan / Alexander J Pak / Dustin R Morado / Gregory A Voth / John A G Briggs /
PubMed Abstract	The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by ...The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.
External links	Proc Natl Acad Sci U S A / PubMed:33397805 / PubMed Central
Methods	EM (subtomogram averaging)
Resolution	9.2 - 16.2 Å
Structure data	EMDB-12147: Immature HIV-1 Gag partial hexamer with 1 Gag subunit missing, obtained by wedge-masked difference map PCA classification Method: EM (subtomogram averaging) / Resolution: 11.8 Å EMDB-12148: Immature HIV-1 Gag partial hexamer with 2 Gag subunits missing, obtained by wedge-masked difference map PCA classification Method: EM (subtomogram averaging) / Resolution: 11.2 Å EMDB-12149: Immature HIV-1 Gag partial hexamer with 3 Gag subunits missing, obtained by wedge-masked difference map PCA classification Method: EM (subtomogram averaging) / Resolution: 16.2 Å EMDB-12150: Immature HIV-1 Gag partial hexamer with 1 Gag subunit missing, obtained by multi-reference classification Method: EM (subtomogram averaging) / Resolution: 10.2 Å EMDB-12151: Immature HIV-1 Gag partial hexamer with 2 Gag subunits missing, obtained by multi-reference classification Method: EM (subtomogram averaging) / Resolution: 10.9 Å EMDB-12152: Immature HIV-1 Gag partial hexamer with 3 Gag subunits missing, obtained by multi-reference classification Method: EM (subtomogram averaging) / Resolution: 11.7 Å EMDB-12153: Immature HIV-1 Gag complete hexamer obtained by multi-reference classification Method: EM (subtomogram averaging) / Resolution: 9.2 Å