wwPDB validation report of PDB entry 6T61

Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot. Refinement was performed iteratively in Phenix and Coot.

CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps

Gag construct was expressed in E.coli and purified using the SUMO-tag system.

Tilt series were low-pass filtered according to their cumulative dose using exposure filters that were calculated using an exposure-dependent amplitude attenuation function and critical exposure constants (as published in Grant & Grigorieff, Elife, 2015). Tilt series were aligned and reconstructed in IMOD.

Data was acquired using a dose-symmetric tilt acquisition scheme, as described in Hagen et al, 2017, J. Struct. Biol, 197(2):191-8

Chimera was used to perform a rigid body fitting of one monomer of 2EIA into the electron microscopy density

The last residues of CA and the first residues of SP (T347-L359) were manually built in Coot

Virus-like-particles (tubular) of EIAV Gag deltaMA-deltap9 (referred to as Gag deltaMA) assembled at pH8.

Subtomogram extraction positions were defined in Amira using the electron microscopy toolbox by determing the radii and the spline of the VLPs. Initially, positions were oversampled and subsequently cleaned during alignments using cross-correlation and distance thresholds.
Subvolumes were defined according to their position on the VLPs

This entry contains the structure for EIAV Gag-deltaMA tubes assembled at pH6

This entry contains the structure for EIAV Gag-deltaMA spheres assembled at pH8

This entry contains the structure for EIAV Gag-deltaMA spheres assembled at pH6

A representative tomogram containing tubes and spheres assembled at pH8

A model of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH8