REL PDBe PDBe PDBe 2014-07-10 2014-08-06 2014-11-05 2015-01-21 The structure of the immature HIV-1 capsid in intact virus particles at sub-nm resolution Schur FKM Hagen WJH Rumlova M Ruml T Mueller B Kraeusslich H-G Briggs JAG immature HIV, Retrovirus, Maturation, capsid, Gag Schur FKM Hagen WJH Rumlova M Ruml T Mueller B Kraeusslich H-G Briggs JAG Structure of the immature HIV-1 capsid in intact virus particles at 8.8A resolution NATURE 517 505 508 2015 25363765 doi:10.1038/NATURE13838 4usn FULLOVERLAP intact HIV-1 particles treated with the protease inhibitor Amprenavir intact HIV-1 particles treated with the protease inhibitor Amprenavir Homohexameric 1 Human immunodeficiency virus 1 Human immunodeficiency virus 1 Homo sapiens VERTEBRATES VIRION SPECIES true false HIV-1 subtomogramAveraging particle 6.5
25mM MES pH 6.5, 150mM NaCl
C-Flat 2/2-2C glow discharged
 ETHANE 100 FEI VITROBOT MARK II Degassed C-Flat 2/2-2C grids were glow discharged for 30 seconds at 20 mA. Virus solution was diluted in PBS containing 10nm colloidal gold. 2 ul of this mixture was applied to a grid. Blotting time: 2 seconds FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.2 4.0 42000.0 FEI TITAN KRIOS AUTOGRID HOLDER Objective lens astigmatism was corrected at nominal working magnification GATAN GIF 2002 2013-08-13 GATAN MULTISCAN 40 -45 60
Subtomogram averaging calculations were performed using the AV3 and TOM packages. Subtomograms were extracted from the surface of the virus.
C6 OTHER 8.8 OTHER TOM, AV3
Reconstruction carried out using subtomogram averaging. Subtomogram averaging was performed using scripts from the TOM (Nickell et al, 2005) and AV3 (Foerster et al, 2005) packages.
32455
Phase flipping of individual tilts
 emd_2706.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 283.5 283.5 283.5 90.0 90.0 90.0 X Y Z -0.72606355 0.87029272 -0.00395048 0.09804771 2.025 2.025 2.025 0.27 AUTHOR Subtomogram averaging reconstruction of the immature HIV-1 capsid from intact virus particles
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 1L6N 1 FLEXIBLE FIT Chimera, MDFF
Structures for the CA-NTD (PDB 1L6N, chain 1) and CA-CTD (PDB 3DS2, one monomer) were rigid body docked into the EM-density using the "Fit in map" option in chimera. The rigid body fit was further refined using Molecular Dynamics Flexible Fitting.
REAL 3DS2 FLEXIBLE FIT Chimera, MDFF
Structures for the CA-NTD (PDB 1L6N, chain 1) and CA-CTD (PDB 3DS2, one monomer) were rigid body docked into the EM-density using the "Fit in map" option in chimera. The rigid body fit was further refined using Molecular Dynamics Flexible Fitting.
REAL
emd_2706.tif