REL PDBe PDBe PDBe 2014-05-01 2014-05-14 2014-05-28 2014-06-25 Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. Bharat TAM Castillo-Menendez LR Hagen WH Lux V Igonet S Schorb M Schur FKM Krauesslich HG Briggs JAG HIV-1, capsid, SP1, helical reconstruction Bharat TA Castillo-Menendez LR Hagen WJ Lux V Igonet S Schorb M Schur FK Krauesslich HG Briggs JA Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PROC.NAT.ACAD.SCI.USA 111 8233 8238 2014 24843179 doi:10.1073/pnas.1401455111 4d1k FULLOVERLAP HIV-1 CANC Y169L/S protein assembled with 73mer DNA into tubular particles HIV-1 CANC Y169L/S protein assembled with 73mer DNA into tubular particles
Helical tubular crystals
helical 1 Human immunodeficiency virus 1 Gag Human immunodeficiency virus 1 HIV-1
10nm protein-A conjugated gold particles were added to the sample. Protein construct consists of CA to NC domains with mutation in position Y169.
Helical true Escherichia coli BL21(DE3) Q5D0H3 helical helicalArray 2 6.0
30 mM MES, 1 mM EDTA, 1 mM DTT, 0.5 M NaCl
300 mesh C-Flat copper grids were glow discharged for 20 seconds
 ETHANE 100 HOMEMADE PLUNGER
Protein stock solutions were dialyzed for 2 h at 4 degree Celsius against the assembly buffer (50 mM Tris HCl pH 7.5) in the presence of nucleic acid
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 -0.001 -0.0045 FEI TITAN KRIOS AUTOGRID HOLDER 2012-12-25 KODAK SO-163 FILM ZEISS SCAI 82 23
Helical reconstruction was carried out as described in Sachse et al, J. Mol. Biol. (2007), based on symmetries determined by sub-tomogram averaging as described in Bharat et al Nature (2012). Averaging of the asymmetric unit was carried out in 3D using methods described in Briggs et al PNAS (2009).
1.92 11.07 C1 9.4 OTHER Spider, AV3
Resolution is calculated using the independently aligned and averaged data sets (gold standard technique)
 emd_2638.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 100 100 100 0 0 0 100 100 100 153.0 153.0 153.0 90.0 90.0 90.0 X Y Z -69.384551999999999 86.176849369999999 2.53140235 19.957006450000002 1.53 1.53 1.53 27.0 AUTHOR Reconstruction of HIV-1 CANC immature-like tubular particles
::::EMDATABANK.org::::EMD-2638::::
 4COP FLEXIBLE FIT Chimera, MDFF
For generating flexible fits of HIV-1 CA, six copies each of the PDB files corresponding to the CA-NTD (PDB 2JPR), and CA-CTD (CA-CTD Y169S, PDB 4COP) were rigid-body fitted into the cryoEM map using UCSF Chimera). The rigid-body fitted structures of the CA-NTD and CA-CTD that corresponded to the same Gag molecule were joined together manually in Coot. This rigid body fit of all proteins was refined using the molecular dynamics flexible fitting (MDFF) package. Secondary structure elements in the input PDB file were constrained during the simulation. The simulation was conducted in an explicit solvent model with periodic boundary conditions.
REAL 2JPR FLEXIBLE FIT Chimera, MDFF
For generating flexible fits of HIV-1 CA, six copies each of the PDB files corresponding to the CA-NTD (PDB 2JPR), and CA-CTD (CA-CTD Y169S, PDB 4COP) were rigid-body fitted into the cryoEM map using UCSF Chimera). The rigid-body fitted structures of the CA-NTD and CA-CTD that corresponded to the same Gag molecule were joined together manually in Coot. This rigid body fit of all proteins was refined using the molecular dynamics flexible fitting (MDFF) package. Secondary structure elements in the input PDB file were constrained during the simulation. The simulation was conducted in an explicit solvent model with periodic boundary conditions.
REAL